Leishmaniasis, caused by parasitic protozoa Leishmania is one of the most important neglected tropical diseases, posing a serious threat to the public health. Leishmania cycle between two different forms in distinct environments: extracellular flagellated promastigotes that proliferate in the mid-gut of female sand flies; and intracellular non-flagellated amastigotes that reside in the phagolysosomes of mammalian macrophages. Our laboratory established host-free differentiation system that mimics the intra-lysosomal environments for L. donovani. Herein, we used this system to investigate the biochemical events occur during differentiation. The signal transduction pathway that initiates the differentiation has not yet been elucidated, but previous investigations on quantitative phosphoproteomics analysis during differentiation revealed that regulatory subunit of protein kinase A (PKAR`) was phosphorylated at early hours of differentiation. This study mainly focused on characterization of new, divergent, regulatory subunit of protein kinase A, named as LdPKAR`. We discovered that PKAR` is anchored to the sub-pellicular microtubule at the cell cortex. Additionally, we showed that this binding to the microtubules is through a formin FH2 domain at the N-terminus of the PKAR`. Further, immunofluorescence analysis revealed that in promastigotes R’ is localized to the proximal region near the cell whereas in amastigotes it surrounds the entire cell cortex. We hypothesized that this distribution of R’ results in the rounding up of amastigotes-shaped cells. Overall, this study gives insights into the role of LdPKAR’ in Leishmania morphogenesis and differentiation.