A culture container transporting set A1 includes: a culture container 1 having a vessel 13 made of a bottom wall 11 and a tubular side wall 12 raised from the bottom wall 11; a flexible cover 2 that covers an upper end 121 of the side wall 12; a presser member 3 that is relatively hard and placed on the cover 2; and a holder 5 that holds the culture container 1, the cover 2 and the presser member 3 integral as stacked into an assembled state, by applying pressure from top and bottom.