The Y chromosome of Drosophila melanogaster is pivotal for male fertility. Yet, only 16 protein-coding genes reside on this chromosome. The Y chromosome is comprised primarily of heterochromatic sequences, including DNA repeats and satellite DNA, and most of the Y chromosome is still missing from the genome sequence. Furthermore, the functions of the majority of genes on the Y chromosome remain elusive. Through multiple genetic strategies, six distinct segments on the Y chromosome have been identified as "male fertility factors," and candidate gene sequences corresponding to each of these loci have been ascribed. In one case, kl-3, a specific protein coding sequence for a fertility factor has been confirmed molecularly. Here, we employed CRISPR/Cas9 to generate mutations, and RNAi, to interrogate the requirements of protein coding sequences on the Y chromosome for male fertility. We show that CRISPR/Cas9-mediated editing of kl-2 and kl-5 causes male sterility, supporting the model that these gene sequences correspond to the cognate fertility factors. We show that another gene, CCY, also functions in male fertility and may be the ks-2 fertility factor. We demonstrate that editing of kl-2, kl-3, and kl-5, and RNAi knockdown of CCY, disrupts nuclear elongation, and leads to defects in sperm individualization, including impairments in the individualization complex (IC) and synchronization. However, CRISPR/Cas9 mediated knockout of some genes on the Y chromosome, such as FDY, Ppr-Y, and Pp1-Y2 do not cause sterility, indicating that not all Y chromosome genes are essential for male fertility.