The yellow (y) locus of Drosophila controls the pattern of pigmentation of the adult cuticle and larval mouth parts. Mutations of y belong to two phenotypic classes; type1 mutants exhibit a total loss of pigmentation from all parts of the cuticle and type 2 mutants show allele-specific mosaic pigmentation patterns. We have cloned y by P-element tagging followed by chromosome walking. We demonstrate that a 2.1-kb transcript which spans 4.6 kb of genomic sequence is the y transcript. The location of this transcript and the putative protein it encodes has been defined by nuclease protection, primer extension and DNA sequencing experiments. A 12-kb genomic fragment containing this transcript along with 2.8 kb of 5'-flanking sequence and 4.6 kb of 3'-flanking sequence is sufficient for the wild-type expression of the larval and adult cuticle phenotypes in germ-line transformants. The majority (12/14) of type1 mutants show structural lesions within exon coding portions of y. Most (6/7) of the type2 structural lesions map 5' to the start of y transcription. One type2 mutant which contains an insertion within the 5'-transcribed but non-translated region appears to have resulted from the internal deletion of a P-element associated with a type1 allele.