The study of sex determination has led to the discovery of a wide array of unrelated master genes controlling sexual fate in many organisms across the tree of life. Beyond addressing fundamental questions in evolutionary biology, characterizing and manipulating master sex genes in insects also holds promise to enable technologies that can form the genetic backbone of area-wide insect genetic control programs. In most organisms, sex determination is determined by the presence, or absence, of a locus on the Y chromosome. Its presence acts as a master switch to define whether an individual is defined early in development as a male or a female. Sex chromosomes are also known to affect many other aspects of an organisms’ biology including the epigenetic regulation of genome-wide expression, fertility and speciation. However, while the content of the X chromosome of most sequenced species has been the subject of study and experimentation, the Y chromosome has been until recently almost entirely a black box. A deeper understanding of Y chromosomes was hampered until recently, because available tools were not adequately suitable for the study of chromosomes that are typically highly heterochromatic and enriched in repetitive elements such as transposons and satellite DNA. This has prevented the identification, characterization and manipulation of unique coding Y loci. Thus, despite its function in sex determination and fertility as well as its role in driving genome evolution, the Y chromosome remains unexplored in most species.