Two nuclear genes from Drosophila yakuba were cloned, the orthologue of the Drosophila melanogaster period (per) clock gene and the orthologue of an unnamed D. melanogaster gene adjacent to per, which encodes a 0.9-kb RNA transcript. The DNA and presumed protein sequences of both genes are presented and compared with their orthologues in D. melanogaster. Consistent with the per orthologues described in other Drosophila species, some parts of the per gene have accumulated nonsynonymous substitutions at a much higher rate than others. This contrasts markedly with the evenly distributed amino acid replacements observed in the protein encoded by the adjacent gene. The level of synonymous and nonsynonymous substitutions between D. yakuba and D. melanogaster per were compared in small subsections across the gene. The results suggest that the divergence observed in the less well-conserved regions of the per protein is principally due to reduced selective constraint, although the limitations of the method used prevent positive selection acting upon a small proportion of sites being ruled out. The level of silent substitution observed in both of these nuclear genes is very similar to the level of silent substitution previously reported between D. melanogaster and D. yakuba mitochondrial genes, confirming several indirect studies, which have suggested that, in contrast to the case in mammals, silent sites are evolving at similar rates in mitochondrial and nuclear genes of Drosophila.