The Yarlung Zangbo River Basin in China has a perennial grass species, Pennisetum centrasiaticum, which shows potential for improving feed quality. Researchers assembled two distinct collections, designated P. centrasiaticum—DB and P. centrasiaticum—NB, to investigate the growth characteristics and genetic variations within this species. Their objective was to comprehend the variance in phenotypic features and to sequence whole chloroplast genomes, which would illuminate evolutionary relationships and possibilities for selective breeding. The scientists assessed both agronomic and nutritional aspects of the grass and used sophisticated high-throughput methods to sequence the whole chloroplast genomes. P. centrasiaticum—DB demonstrated beneficial traits, including increased height (71.58 cm), a greater number of internodes (4.17), elongated ears (9.33 cm), an elevated ear weight ratio (7.91%), and higher ether extract content (16.40%), alongside reduced crude fiber content (386.30 g/kg), indicating improved palatability. The chloroplast genomes of P. centrasiaticum—DB (138,291 bp) and P. centrasiaticum—NB (138,283 bp) exhibited standard four-part architectures, with minor variations in the LSC, SSC, IR sections, GC content, and SSR distribution. A phylogenetic study classified Pennisetum and Cenchrus into separate clades, confirming their distinction at the species level. The differences in agronomic data and chloroplast genome data further clarify the distinctions between these two types of P. centrasiaticum, providing theoretical support for their future utilization. The P. centrasiaticum—DB germplasm has significant potential for producing high-quality fodder, while the chloroplast genome data provide fresh insights into the evolutionary linkages and molecular evolution of Pennisetum species.