There are 99 Seeds scattered throughout this massive game. Every 20 seeds you give to the Pipot you receive a reward (rewards listed below). If you miss any seeds from locations that you can't access again you can buy them from the Auction House in Saman. Collecting all 99 seeds is a requirement to complete the Skill Master (as you need Pipot Collar) and to get the Treasure Trove Achievements.
The seeds are listed in the order of when you are first able to acquire them (more or less). Your actual order may vary.
Number of Seeds Reward 20 Seeds Adamantis Adamantis Ring 40 Seeds Earth Charm 60 Seeds Power Bangle 80 Seeds Gigantes Brooch 99 Seeds Pipot Collar
Zone Name Description 01 Uhra - The Great Gate On top of the guard tower inside a can. 02 Uhra - The Great Gate Station Behind a poster on the northern end behind two chatting soldiers 03 Uhra - Central Station Square To the left of the fountain next to the bench in the black can. 04 Uhra - Central Station Square Behind a poster at the entrance of the blocked alleyway on the way to main street. 05 Uhra - Main Street Found behind the poster after the first step in Uhra Main Street 06 Uhra - Main Street Across the street outside the inn there's a black object close to the screen 07 Uhra - Tolsan's Inn In the pot on the stairs 08 Uhra - Virno's Tavern The lower of two pots on 2nd floor (US) [which is 1st floor (British)]. 09 Uhra - Residential Area On the left side of the park, behind a poster near the steps 10 Uhra - Residential Area North of the park in a black can 11 Uhra - Residential Area North of the park, in a garbage can between two gold pots 12 Uhra - Residential Area North of the park, in a gold pot (to the right of seed 11) 13 Uhra - Gongora's Mansion - Magic Research Lab Kick the can in the North East corner of the zone. 14 Ipsilon Mountains - Valley Road Ram into a tree on the right side just north of the Save Orb 15 Ipsilon Mountains - Valley Road A tree on the right side, you can see two pots in the background from here 16 Ipsilon Mountains - Near Mountain Hut In a tree on the right where the path opens up 17 Ipsilon Mountains - Near Mountain Hut In the second tree on the left overlooking the cliff 18 Ipsilon Mountains - Mountain Hut In a pot on the right side of the bottom floor 19 Ipsilon Mountains - Cart Track Ram a cart after you have push the cart 20 Grand Staff Construction Base - Building Material Warehouse Complete the Roshion's Short-Cut quest to gain access to the warehouse. The seed is in pot inside. 21 Sea of Baus - Reef Shallows In a clam on the winding path (Available at Auction House on Disc 4) 22 Sea of Baus - Beach of the Wastes First machine you see (Available at Auction House on Disc 4) 23 Sea of Baus - Beach of the Wastes In a machine on the right hand side on a sandbar (Available at Auction House on Disc 4) 24 Numara - Numara Palace Facade On the left side of the facade up the stairs but underneath the ramp. 25 Numara - Numara Palace Facade On the right side of the facade up the stairs but underneath the ramp. 26 Numara - White Square North end of the area on the right in a vine. 27 Numara - White Square In the vine next to were Chuchu is originally standing south of the inn. 28 Numara - Thelran's Inn In the glowing plant to the left of the innkeeper 29 Numara - Thelran's Inn In the glowing plant to the right of the innkeeper 30 Numara - Thelran's Inn In a flower pot on the 2nd floor first room to the left 31 Numara - Main Street In a vine next to Chuchu (before you start the quest) 32 Numara - Main Street In a vine on a wall by the Artists' Salon 33 Numara - Main Street In a vine on the left side of Ninn's Boutique 34 Numara - Main Street In a vine at the end of the ally (next to the ladder) on the left side of Ninn's Boutique 35 Numara - Main Street In a vine next to the back door to Nalia's Item Shop 36 Numara - Ninn's Boutique A plant in the back corner of the shop (to the left and on the other side of the barrier to the show room). 37 Numara - Nalia's Item Shop After completing Lonely Chuchu's Treasure you can get into the back room from the street. The seed is in a drawer in this room. 38 Numara - Canal Street Right after you cross the bridge in a vine on the right side. 39 Numara - Canal Street A fruit in a tree on the left side of the street after you cross the 2nd bridge. 40 Ghost Town - Funeral Procession Beach In a pot next to the house north of the pipot. 41 Crimson Forest - Maze of Gloom In a mushroom on the left side just before the entrance to the Near Swamp zone. 42 Crimson Forest - Near Swamp In a stone pillar in the center.
Zone Name Description 43 Crimson Forest - Maze of Gloom Once Mack rejoins your party, use the 1st elevator you come to. The seed is found in a stone pillar after the tree bridge. 44 Numara Palace - Corridor Garden On the right side of the first floor in a pot. 45 Numara Palace - Corridor Garden In a pot to the left (but not right next to) the lift on the north side of the first floor. 46 Numara Palace - Corridor Garden In a pot to the left (but not right next to) the lift on the north side of the second floor. 47 Numara Palace - Corridor Garden In a pot on the left side of the room by the lift on the second floor. 48 Mountain Village of Tosca In a pot near the waterfall. 49 Tosca - Tolty's Inn In a closet up stairs (the room to the left) 50 Tosca - Tolty's Inn In a closet up stairs (the room to the right) 51 Tosca - Deeno Family House A pot on the 2nd floor. 52 Black Cave - Maze of Darkness The upper level you'll need to jump across a gap for the chest. 53 Black Cave - Helltrap Next to the Save Orb before you enter The Great Hall of Foul Creatures 54 City of Saman - Main Street In a pot next to the street stand. 55 City of Saman - Main Street In a pot next to Audun's Item Shop. 56 City of Saman - Erlio Family House In a pot on the left side of the house. 57 City of Saman - Kersen's Inn In a pot on the right side of the guest room on the first floor 58 City of Saman - Kersen's Inn In a pot on the right side of the guest room on the second floor 59 City of Saman - Emelo's Tavern In a pot at the northern end of the tavern. 60 City of Saman - Audun's Item Shop In a pot inside the shop. 61 Experimental Staff - Samanese Merchant Ship In a closet on the ship. (Available at Auction House on Disc 4)
Zone Name Description 62 Ice Canyon - Ice Gorge On the left side in a chest up a ramp 63 Ice Canyon - Blizzard Peak Walk past the 3 wind tunnels and slide down to get to the chest 64 Gohtza - Rosa's Restaurant In a pot inside the Restaurant. This location becomes unavailable after Gohtza Freezes (Available at Auction House on Disc 4) 65 Gohtza - Abandoned Apartment - 9th Floor In a pot at the base of the stairs (access from stairway entrance to 10th floor to the right of elevator entrance around the back of the building) 66 Gohtza - Abandoned Apartment - 9th Floor In a panel on the wall right across from the previous seed 67 Gohtza - Abandoned Apartment - Bargel's Inn In a pot beside the counter 68 Gohtza - Gohtza Station - Waiting Room In a pot next to the ticket counter (Available at Auction House on Disc 4) 69 Uhra - Back Alley Keep left when entering the area and you will find it in a gold pot 70 Uhra - Back Alley Take the north most path after the Save Orb and then kick a metal pillar 71 Uhra - Barkus' Arms and Armor Emporium Enter from the top floor and go to the gold pot at the bottom of the steps 72 Uhra - Back Alley In a pot in the ally behind Tolsan's Inn 73 Uhra - Back Alley - Near Castle Turn right when entering the area, go up a ladder and it's in the first gold pot you see 74 Snow Covered Trail When you have only Cooke and Mack go to a tower on the right side it's in a chest by a Save Orb (Available at Auction House on Disc 4) 75 Old Gohtza - Eastern District In a metal pipe right before you change zones to the East-bound Track while you are controlling Jansen (Available at Auction House on Disc 4) 76 East-bound Track In the 3rd box on the right side while controlling Jansen (Available at Auction House on Disc 4) 77 Uhra Sewers - Treatment Plant In a pot in the northeast side of the zone. (Available at Auction House on Disc 4) 78 Uhra Sewers - Treatment Plant In a pot before the door to Magic Tank Upper Division (Available at Auction House on Disc 4) 79 Uhra Sewers - Conduit A pot in the 3rd conduit (Available at Auction House on Disc 4) 80 Gohtzan Refugee Camp North of the Save Orb in a pot by the Lodging Tent 81 Crashed Magic Train Site A glowing object in the snow on the left side of the path 82 Burning Cave - Path of Steam In a chest in a dead end on the right side of the zone. 83 Burning Cave - Path of Poison Mist In the first geyser you come to (grab it when the geyser isn't spraying water)
Zone Name Description 84 Uhra - Monorail - The Castle Station The top of the two pots on the left side of the area. 85 Uhra - Castle of Uhra - Station Square In a chest near the monorail 86 Uhra-Gongora's Mansion - Secret Cave Jump over 2 gaps. The chest is behind a wall that you can ram on the north side. 87 Numara - Chamber of Flowers In a closet on the left side of the room 88 Numara - Winds Chamber On the right side of the room in a closet in the back 89 Numara - Waves Chamber On the right side of the room in a closet in the back 90 Numara - Queen's Chamber A pot in the south western corner of the room 91 Numara - Port of Numara - Terminal Building In a locker (bottom floor) on the right side of the terminal 92 White Boa - Brig Go down to the cell you were in previously. The seed is in the cell next to it (which is now open). 93 Pirate Fortress Ride the gondola down, climb up two ladders and look inside the second pot on the right 94 Kelolon Village In a pot near the tournament area 95 World Map - Underwater 1 on the Underwater Map. Submerge the Nautilus and look for bubbles, press A when you get close to them. 96 World Map - Underwater 2 on the Underwater Map. 97 World Map - Underwater 3 on the Underwater Map. 98 World Map - Underwater 4 on the Underwater Map. 99 World Map - Underwater 5 on the Underwater Map.
To find the Five Underwater Seeds , follow the link to the Underwater Map. Or view the map below.