Germ line development requires coordination of cell type-specific transcription and preparation for meiosis. In Drosophila spermatogenesis, over a thousand of male germ line-specific genes are transcribed in spermatocytes, before meiosis, in preparation for the post-meiotic spermiogenesis. While doing so, a chromosome-level chromatin reorganisation takes place to pair duplicated chromosomes to successfully pass down each one of the chromosomes to haploid cells after meiotic cell divisions. We identified duplicated paralogs of RNA polymerase II associated factor 1 (PAF1) subunits that are specifically expressed in the testis of fruit flies Drosophila melanogaster; hence we named the complex tPAF. The four core subunits of tPAF, namely, tPaf1, tLeo1, tCdc73, and tCtr9 are each essential for male fertility. RNAseq analysis of the mutant testes did not reveal a large-scale change in the transcription of spermatocyte-specific genes whereas the mutant testes displayed strong defects in meiotic chromosome segregation. Interestingly, we found that tPAF is required for the transcription elongation of the gigantic genes kl-3 and kl-5 on the Y-chromosome. These kl genes are mega-base long, transcribed across two-thirds of the spermatocyte development (~3 days), and the completion of transcription and splicing marks the onset of meiosis. I discuss how the kl gene transcription might act as a timer for spermatocyte development, failure of which leads to a mis-coordination of meiotic chromosome segregation.