A cap for a microtube, which can be automatically aligned by an alignment plate for insertion in a correct orientation into the open end of the microtube held in a micro tube rack. The plate has partitions in a grid which produces a matrix of cells having a pitch defined by the spacing between the partitions. The cap 100 has an plug portion 120, which is adapted to be inserted into the open end of the microtube which is held in a rack having a matrix of wells congruent with the matrix of cells in the alignment plate. A grip portion 110 of the cap has an outer circumferential diameter larger than an outer circumferential diameter of the plug portion 120, so that when the cap is inserted in the microtube, the grip portion protrudes from the open end of the microtube. The entire length of the cap 100 is longer than the pitch of the alignment plate and shorter than twice the pitch. An upper edge of the grip portion 110 of the cap 100 has a collar 130 with an outer circumferential diameter larger than the diameter of the cells of the alignment plate. The plug portion 120 of the cap 100 has a taper 122 which is tapered toward a front end, and the center of gravity of the cap 100 is in the plug portion, so that the plug portion of the cap gravitates into one of the open cells of the alignment plate.