The white, brown, and scarlet genes of Drosophila melanogaster encode three proteins that belong to the Traffic ATPase superfamily of transmembrane permeases and are involved in the transport of guanine and tryptophan (precursors of the red and brown eye pigments). We have determined the nucleotide sequences of two mutant white alleles (wco2 and wBwx) that cause reduced red pigmentation but have no effect on brown pigmentation. In wco2 the effect is only observed when interacting with the bw6 allele or a newly isolated allele (bwT50). These alleles of the brown gene were cloned and sequenced. In wco2 the codon for glycine 588 is changed to encode serine; in wBwx the triplet ATC encoding isoleucine 581 is deleted; asparagine 638 is changed to threonine in bw6, and glycine 578 is changed to aspartate in bwT50. No other relevant changes to the gene structures were detected. P-element-mediated germline transduction was used to construct a fly strain containing a white gene with a mutation of the nucleotide binding domain. Such flies had white eyes, indicating that the mutated white gene was unable to support either guanine or tryptophan transport. The implications of these mutations are discussed in terms of a model of the Drosophila pigment precursor transport system.