We have prepared reference polytene photographic maps as a standard sequence for the Drosophila bipectinata complex using structurally homozygous flies derived from a stock of Drosophila parabipectinata from Brunei, Borneo, in 1971. We found 87 inversions in the D. bipectinata complex and described their breakpoints on the reference maps. Only 2 arrangements were shared interspecifically: 2R-AB was shared with 3 species, D. parabipectinata, D. bipectinata, and Drosophila malerkotliana, and 3L-A was found in 2 species, D. parabipectinata and D. malerkotliana. The 2 subspecies of D. malerkotliana and the 2 subspecies of Drosophila pseudoananassae shared half of the total gene arrangements detected in each species. The number of different inversions found between species in the complex ranges from 7 (between D. parabipectinata and D. malerkotliana) to at least 24 (between D. bipectinata and D. pseudoananassae). On the basis of the characteristic differences of their gene arrangements, we propose a reliable chromosomal phylogeny of the D. bipectinata complex.