Crater
The crater on Xeroph Isle holds Komodo Dragon, Dancing Flame and Skullgon monsters during the day, and Chimera and Frostburn monsters at night. The darkonium crystal is inside the blue chest in this location.
Xeroph Shrine
This location includes the Bag o' Laughs, Hammerhood and Mummy Boy monsters. However, taking the wrong turn can get you lost, in which case you may encounter Dessert Demon and Imp monsters. The darkonium crystal is located in a blue chest just before the nexus chamber.
Madame Rummy's Garden
The third crystal is located across the sixth drawbridge in Madame Rummy's Garden. This location also features Capishum, Sea Urchin, Spike Hare, Goodybag, Dragonthorn, Khalamari Kid and King Kelp monsters by day. By night, you may see Shell Slime, Chanine, Seasaur and Angel Slime monsters.
Palaish Shrine
Darkonium crystal number four is located on the fourth floor of the Palaish Shrine. This area contains Lump Wizard and Fencing Fox monsters only. The blue chest is located just before the Shrine's nexus chamber.
Madame Rummy's Garden Part 2
To find the fifth crystal, revisit Madame Rummy's Garden. Follow the path to the right to find the blue chest.
Infern Isle
The sixth crystal is on Infern Isle. You will face Flyguy, Skelton, Walking Corpse and Metal Slime Knight monsters during the day and Dark Slime Knights at night. Head left, then follow the path till it splits and take the right-hand path to reach the blue chest.
Celeste Isle
You can find the seventh darkonium crystal in the ruins on the southern portion of Celeste Isle. This area also contains brown and red chests with useful items.
Infant Isle
Unlock the gate on Infant Isle to visit a new area. Here you will face Hades Condors during the day, and Winky and Slime monsters at night. Head across the rope bridge to the blue chest to get the eighth crystal.
Celeste Isle, North
You will visit the northern part of Celeste Isle with the help of Great Looking Glass. Before you enter the nexus chamber, visit the blue chest to get the ninth crystal.
Fert Isle
The last darkonium crystal is on Fert Isle. During the day, this location is protected by Argon Lizard, Frogface, Metal Slime, Hell Hornet, Hades Condor, Scissor Beetle, Bodkin Archer, Hacksaurus, Great Argon Lizard, Beetle Boy, Goreilla and Boss Troll Monsters. At night, you may encounter Mud Mannequin, Lump Wizard, Dingaling, Hellhound, Giant Moth, Treeface, Jargon, Fang Slime and Wailin' Weed monsters. The crystal is in a blue chest across the bridge and up the ladder.