Alfalfa (Medicago sativa L.) is an important forage crop worldwide. However, little is known about the effects of breeding status and different geographical populations on alfalfa improve-ment. Here, we sequenced 220 alfalfa core germplasms and determined that Chinese alfalfa cultivars form an independent group, as evi-denced by comparisons of FST values between different subgroups, suggesting that geo-graphical origin plays an important role in group differentiation. By tracing the influence of geographical regions on the genetic diversity of alfalfa varieties in China, we identified 350 common candidate genetic regions and 548 genes under selection. We also defined 165 loci associated with 24 important traits from genome-wide association studies. Of those, 17 genomic regions closely associated with a given phenotype were under selection, with the un-derlying haplotypes showing significant differ-ences between subgroups of distinct geo-graphical origins. Based on results from expression analysis and association mapping, we propose that 6-phosphogluconolactonase (MsPGL) and a gene encoding a protein with NHL domains (MsNHL) are critical candidate genes for root growth. In conclusion, our results provide valuable information for alfalfa im-provement via molecular breeding.