Seven paracentric inversions, designed i1 to o1, on polytene chromosome arm 2 and one, r, on chromosome arm 3 were found in natural populations of the Anopheles culicifacies complex. Of the polymorphic inversions on chromosome arm 2, one was found in species B, whereas all others were in species A and the r inversion on chromosome arm 3 was found in both the species. One inversion on chromosome arm 2, the i1 inversion, was observed at low frequency in parts of northern India and as a cline of progressively higher frequencies towards central India. In southern India, there was no specific pattern of i1 distribution, with most localities showing Hardy-Weinberg equilibrium frequencies. Significant deficiencies of i1 heterozygotes in a few populations, mostly towards the northern end of the cline, indicate a second species within species A. The same inversion may be floating in one species and fixed in the other; thus, the two species are homosequential for polytene chromosome arrangements. These data support a recent report of species D within this group, but polytene chromosome arrangement cannot be used to identify species A and D at an individual level.