Despite its function in sex determination and its role in driving genome evolution, the Y chromosome remains poorly understood in most species. Y chromosomes are gene-poor, repeat-rich and largely heterochromatic and therefore represent a difficult target for genetic engineering. The Y chromosome of the human malaria vector Anopheles gambiae appears to be involved in sex determination although very little is known about both its structure and function. The work described in this thesis led to the characterization of an Anopheles gambiae transgenic strain obtained by transposase-mediated integration of a transgene construct onto the Y chromosome. Using meganuclease-induced homologous repair a site-specific recombination signal was introduced onto the Y chromosome and the resulting docking line, named YAttP, was proven to allow secondary integration. To demonstrate its utility, the activity of a germline-specific promoter when located on the Y chromosome was studied. Anopheles arabiensis is another important vector of human malaria. Since active insertions onto the Y chromosome are extremely rare, a scheme based on crossing and selection was used to overcome F1 hybrid male sterility and introgress the modified Anopheles gambiae Y chromosome in the Anopheles arabiensis genetic background. Fertility of Y-introgressed males, tested after up to 10 backcross generations, was comparable to fertility of wild-type Anopheles arabiensis males. The molecular manipulation of the Y chromosome in Anopheles gambiae, opens up a number of ways to explore one of the most fascinating of evolution's upshots and its introgression in the Anopheles arabiensis genetic background may answer important questions on the similarity and differences in Y chromosome biology of closely related species. The Y-linked fluorescent transgenes allow automated sex separation of these important vector species, providing the means to generate large single-sex populations. Furthermore, the possibility of introducing genes of interest specifically onto the Y chromosome makes these strains a valuable tool for vector control strategies.