The study presents a method for de novo assembly of the *Aedes aegypti* genome using Hi-C data, which yields chromosome-length scaffolds. The method combines Hi-C data with existing draft assemblies to generate high-quality, accurate genome assemblies. The approach is validated by assembling a human genome de novo from short reads alone (67× coverage). The method is then applied to create genome assemblies of *Ae. aegypti* and *Culex quinquefasciatus*, both consisting of three scaffolds corresponding to the three chromosomes in each species. The assemblies indicate that most genomic rearrangements occur within, rather than between, chromosome arms. The procedure is fast, inexpensive, and accurate, making it applicable to many species. The study also explores the evolutionary relationships among the genomes of *Aedes*, *Culex*, and *Anopheles* mosquitoes, suggesting that each chromosome arm in these species descends from a single arm present in their common ancestor about 150 to 200 million years ago.The study presents a method for de novo assembly of the *Aedes aegypti* genome using Hi-C data, which yields chromosome-length scaffolds. The method combines Hi-C data with existing draft assemblies to generate high-quality, accurate genome assemblies. The approach is validated by assembling a human genome de novo from short reads alone (67× coverage). The method is then applied to create genome assemblies of *Ae. aegypti* and *Culex quinquefasciatus*, both consisting of three scaffolds corresponding to the three chromosomes in each species. The assemblies indicate that most genomic rearrangements occur within, rather than between, chromosome arms. The procedure is fast, inexpensive, and accurate, making it applicable to many species. The study also explores the evolutionary relationships among the genomes of *Aedes*, *Culex*, and *Anopheles* mosquitoes, suggesting that each chromosome arm in these species descends from a single arm present in their common ancestor about 150 to 200 million years ago.