Restriction map polymorphism at two X linked loci, forked and vermilion of Drosophila melanogaster was studied in three natural populations. The estimates of nucleotide variation were θ = 0.003 and π = 0.002 for the forked region and θ =0.004 and π =0.002 for the vermilion region. Three insertions (>500 bp) were observed at each locus. Typical of other regions of this species each of these large insertions was unique in the sample. Non-random association among polymorphisms was common at the vermilion locus, while the forked locus was not polymorphic enough to test linkage disequilibrium. The amounts of restriction site and size variation in the vermilion and forked were within the range observed for other loci of D. melanogaster.