Red Crystal: A Pirate's Home (South America). There is a stone to push. There is a downward staircase under the stone, and there is one in the treasure chest below.
Green Crystal: There is a village called テドン (that is, a small town where dark light can be found). Not during the day, but at night, which can be obtained by talking to people in the cell.
Blue Crystal: If you walk on the bottom of the trial hole (the kind where only one person enters), you will hear the cry of "going back" constantly. No matter the sound goes forward, there is still one of the two treasure boxes in the end.
Topaz: In the town built by the merchant's companion, the plot developed to the point where the merchant was put in prison and was investigated behind the throne.
Yinjing: Go through the cave in the south of Demon City (the one that can only enter after paving the way with the sword of the earth) and reach a small temple where you can talk to the Oracle.