Two V3 vitellogenin clones isolated from genomic libraries of Drosophila grimshawi (G1, Auwahi, Maui) were found to differ in length. Structural comparison of the two clones established that the length difference could be attributed to two insertions/deletions of about 200 bp each, both within the 3' flanking sequences of the gene. The two length variants appeared to be polymorphic in the G1 laboratory strain, as demonstrated by analysis of genomic DNA isolated from single flies. The deleted variant sequence was traced by further analysis to two other D. grimshawi strains (PK9 and S10G1) which originated from the island of Molokai. The existence of this morph in the Maui strain appears to have resulted from a laboratory stock contamination at the Drosophila Stock Center. In the course of a few generations of culture of this G1 strain at New York University, the deleted morph increased its frequency surprisingly rapidly, almost replacing the original morph, while at the Bowling Green Stock Center, the original morph still predominates. These frequency changes are most likely consequences of genetic drift due to bottlenecks in the maintenance and propagation of this stock.