This data set contains frequencies of the (Thr-Gly)17 and (Thr.Gly)20 period allele (Frequency17 and Frequency20) for 18 Drosophila melanogaster populations collected in 2004 and for 16 populations collected 2002 (Fig. 1). When using this data, please cite the original publication: Weeks, A. R., McKechnie, S. W. and Hoffmann, A. A. (2005). In search of clinal variation in the period and clock timing genes in Australian Drosophila melanogaster populations. Journal of Evolutionary Biology 19: 309-656