Pea (Pisum sativum L.) is an important legume crop that is widely grown worldwide for human consumption and livestock feed. Despite extensive studies, the population genetic structure and classification of cultivated and wild pea (Pisum sp.) are remaining controversial. To characterize patterns of genetic and morphological variation and investigate the classification of Pisum, we conducted comprehensive population genetic analyses for 323 accessions from cultivated and wild pea representing three species of Pisum utilizing 34 morphological traits and 87 polymorphic SSR markers. First, we identified three distinct genetic groups among all samples. Group I was primarily composed of Pisum fulvum, Pisum abyssinicum and some wild P. sativum accessions, whereas groups II and III consisted of the two genetic groups under P. sativum representing different geographic distributions of cultivated pea. Analyses of morphological variation revealed significant differences among the three species. Second, among pea germplasms representing eight taxa of Pisum, P. fulvum and P. abyssinicum possessed unique genetic backgrounds and morphological characteristics, corroborating their independent species status. The intraspecific subdivisions of P. sativum described by some authors were not supported in this study, with the exception of several genotypes of P. sativum subsp. elatius that were clustered with P. fulvum and P. abyssinicum. Finally, we confirmed that the Chinese pea germplasm was genetically distinct and could be divided into two genetic groups, each of which included both spring-sowing and autumn-sowing ecotypes. These results provide a robust foundation for understanding pea domestication and the utilization of wild genetic resources of pea.