We report the results of a phylogenetic survey of the retrotransposon copia in the melanogaster subgroup of the Drosophila genus. The polymerase chain reaction was used to amplify the copia 5' long terminal repeat and the adjacent untranslated leader region from representative melanogaster subgroup species. Restriction and sequence analyses of this region reveal discrete classes of copia size variants within the melanogaster subgroup. Phylogenetic comparisons of copia sequence data indicate that the size variants represent different copia subfamilies which diverged prior to their distribution in the melanogaster subgroup. Our results also suggest that copia elements have been subject to horizontal and vertical transmission during their evolution.