Pearl millet (Pennisetum glaucum (L.) R. Br.) and napier grass (Pennisetum purpureum Schumach) are the most economically important species in the genus Pennisetum. Knowledge of genetic diversity of these two species would enhance their potentials for utilization. The present work assessed the genetic diversity and phylogenetic relationship among Nigerian and Indian accessions of pearl millet and napier grass using microsatellite markers. We extracted genomic DNA from each accession and carried out Polymerase Chain Reaction using Inter-Simple Sequence Repeat markers. Data obtained were analyzed for genetic diversity using MEGA 4.0 software. A total of 48 loci consisting of 410 bands were generated with 56.25% polymorphism. Principal Coordinates analysis revealed three principal axis contributed significantly (70.20%) to the observed variations. Accessions of napier grass from Nigeria and India were plotted on a coordinate plane while pearl millets from both countries co-existed on different quadrants. Cluster analysis, showed that Nigeria and India accessions of napier grass were similar. Consistent link of COM-CO-3 with Nigeria napier grass and millet accessions suggested a common progenitor. The polymorphism obtained in this study showed that ISSR is an effective marker for assessment of genetic diversity and the connection between most accessions indicated that they have common progenitor.