The Trypanosomatidae are early-diverged protozoan parasites, including human pathogens Trypanosoma brucei and Leishmania major. Within these parasites, hundreds of genes with unrelated functions are organized into long arrays throughout the genome, transcribed polycistronically by RNA polymerase II (RNAPII). Little is known about transcription termination in Trypanosomatids. Epigenetic marks, including base J, are enriched at RNAPII transcription termination regions in T. brucei and Leishmania spp., playing a critical role in transcription termination. The study of base J function led to the identification of the PJW/PP1 complex in L. tarentolae, composed of PP1, PNUTS, Wdr82, and the base J-binding protein JBP3. Ablation of these protein factors results in readthrough transcription at the end of gene arrays in T. brucei and L. major, indicating that the PJW/PP1 complex regulates transcription termination in Trypanosomatids. Unexpectedly, we discovered that in T. brucei, the PJW/PP1 complex is also essential for terminating antisense transcription from bidirectional promoters, ensuring transcriptional directionality, and for monoallelic expression of variant surface glycoprotein (VSG). Further exploration into the mechanism by which the complex regulates transcription termination revealed PP1-dependent phosphatase activity toward RNAPII C-terminal domain (CTD), implicating CTD dephosphorylation at the end of gene arrays in regulating transcription termination. Additionally, our analysis of the intramolecular architecture of the PJW/PP1 complex focused on the role of PNUTS. PNUTS, as a scaffolding protein within the complex, mediates PP1 association with a central sequence containing conserved short linear motifs (SLiMs), specifically RVXF-ɸɸ-F motifs, and binds to Wdr82/JBP3 with its C-terminus. Despite the presence of eight PP1 homologs in L. tarentolae, PNUTS preferentially binds to PP1-8, discriminating between homologs based on their C-terminal tails and specific inserts within their catalytic core regions. Consistent with its role as a scaffolding protein, PNUTS protein levels must be finely tuned for complex integrity. These findings illuminate the process of transcription termination in trypanosomatids and establish a mechanistic link between base J and transcription termination.