Studies of the salivary gland chromosomes of many strains of Drosophila pallidipennis, with various cross-tests, has revealed that of the five rodlike chromosomes only one autosome (D) has undergone important inversions and the X chromosome exhibits special behavior (such as little variation of the strong parts and weaker pairing), and that the group is a complex rather than a single species. There are two separate Mendelian populations, the hybrids of which display more or less strong degrees of breakdown in gene coadaptedness (the minimum being complete F1 male sterility). Whether they are full species (through complete assortative mating when mixed) remains to be verified. One of these forms (centralis), occupying Central America and Colombia, is monomorphic for a CE gene arrangement of the D chromosome. In the other form (true pallidipennis) the CE gene arrangement occurs only in Peruvian populations and is completely lacking in Bolivia, Venezuela and Brazil, where local populations are mono- and polymorphic for rearrangements, each of which can only result from an inversion in the CE chromosome. It is suggested that selection is in the process of eliminating the CE arrangement in pallidipennis. This interesting situation, combined with the very high quality of breeding and chromosomal cytology of the flies, should prove valuable for studies in developmental and population genetics.