Legumes are excellent sources of protein and oil for human and animal nutrition. Moreover, they are unique among other cultivated plants for their ability to form nitrogen-fixing symbiosis with rhizobia. Medicago truncatula Jemalong A17 (hereafter A17) and Medicago littoralis R108 are widely adopted in legume biology as model organisms. Here, using long-read sequencing, we generated gap-free genome assemblies for these two accessions. Complete assemblies of all centromeres reveal that Medicago centromeres are composed satellite repeat arrays. The A17 centromeres are featured with two satellite repeats, whereas the R108 centromeres mainly contain only one repeat, highlighting the lineage-specific evolution of centromeres. Our study provides new insights into plant centromere evolution, but also valuable resources for functional genomics in legumes.