The object of the present invention is to provide a cell culture vessel having a plurality of microwells, which allows to identify the position of a microwell by observing it under a microscope without moving a viewing position, which has identifiers to be easily disposed to the microwells. The present invention is directed to a cell culture vessel comprising a bottom and a sidewall, in which the bottom has a cell containing section in which a plurality of microwells for containing cells are disposed, identifiers are disposed in the vicinities of the plurality of microwells so as to make pairs in individual microwells, and the relative position of each of the identifiers to a partner microwell varies in every pair.