Honey bee (Apis mellifera) wing measurements are often used to discriminate lineages and subspecies. The precision and repeatability of the measurements depends on various factors, including seasonal variation, and differences between left and right wings. The seasonal variation of the cubital index, which is the proportion of two vein lengths, has been investigated, but subspecies can be identified through geometric morphometrics. This method allows both wing size and shape to be determined and analyzed separately. We studied changes in the wing size and shape in consecutive months between June and September as well as the differences between the left and right wings. We found that wing size differed significantly among colonies, months and body sides, but shape differed significantly only among colonies and months but not among body sides. There was also a complicated pattern of interactions between various factors. The seasonal differences in wing shape were much smaller than the differences among colonies and their influence on identification of honey bee lineages was relatively small.