The allozyme genetic variability of various species is correlated with a variety of morphological, physiological and fitness-related traits. In particular, temperature can affect the fitness of insects through its influence on enzyme function. We examined the seasonal (12 days over 1 year) and daily (nine samples over each day) allozyme variation at the phosphoglucomutase (PGM) locus in one population of yellow dung flies (Scathophaga stercoraria; Diptera: Scathophagidae). PGM is of central functional importance in the mobilization of glycogen reserves for flight, and has been shown to affect larval growth at different temperatures in the laboratory. Based on a sample of over 3000 flies, we found a quadratic relationship, with a minimum at ~12 °C, between the frequency of the most common allele and temperature, primarily mediated by seasonal temperature variation. This could be caused by behavioural responses over the short-term, but over the year either variable viability or sexual selection probably operates on this locus, maintaining the existing polymorphism. These results call for further work on the functional differences between PGM allozyme genotypes.