We provide evidence that sex chromosomes in *Ae. aegypti* are genetically differentiated between males and females over a region much larger than the sex-determining region (SDR). Our linkage mapping intercrosses failed to detect recombination between X and Y chromosomes over a 123-Mbp region (40% of their physical length) containing the SDR. Sex-differentiated genomic region was associated with a significant excess of male-to-female heterozygosity and contained a small cluster of loci consistent with Y-specific null alleles.