Members of the retrotransposon family micropia were discovered as constituents of wild-type Y chromosomal fertility genes from Drosophila hydei. Several members of the micropia family have subsequently been recovered from Drosophila melanogaster and four micropia elements, micropia-DhMiF2, -DhMiF8, -Dm11 and -Dm2, two each from D. hydei and D. melanogaster, have been totally sequenced (17 kb of micropia sequences and 6.8 kb from insertions). Comparative analysis of micropia sequences revealed a complex pattern of divergence within a single Drosophila genome. The divergence includes deletions, possibly by a slipped mispairing mechanism, insertions of a retroposon, and of another retrotransposon (copia) and "positional nucleotide shuffling" within the tandem repeats of the 3' non-protein-coding region of micropia elements. A 10 bp long sequence of each repeat unit of the 3' tandem repeats of micropia elements is highly conserved and is therefore a candidate of functional importance either in transposition events or in regulatory activity on flanking DNA sequences.