Variation within a 12-kb region of the second chromosome of Drosophila melanogaster which includes the Adh transcriptional unit was studied in 59 isochromosomal lines drawn from two populations. A number of restriction-fragment length polymorphisms due to both restriction-site presence/absence and insertions/deletions were revealed and the proportion of polymorphic nucleotides was estimated as 0.017 in population "Chateau Tahbilk" and 0.025 in population "Groningen." The presence within population Groningen of two complementary haplotypes at a high frequency was noted and its possible origin is discussed. The distribution of insertion/deletion variants within the populations was consistent with an associated deleterious effect and significant clustering of such variants to a 1-kb region approximately 4 kb from the transcriptional unit was also revealed. Analysis of gametic disequilibrium showed that its intensity was not related to the physical distance separating the markers on the chromosome and that strong disequilibria may flank weaker disequilibria. Two alternative interpretations of these data are advanced based upon natural selection and the hitchhiking effect of a favorable mutation. Comparisons of gametic disequilibrium among the four populations now surveyed at this locus were made using model fitting by weighted least squares and several significant contrasts were revealed.