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Snap bean (Phaseolus vulgaris L.) is the vegetable form of common bean, and regarded as one of the most important and commonly consumed products in the world. In this study, 221 snap bean core accessions mostly from China were characterized the genetic diversity, gene pool identity, and relationships using 30 microsatellite markers, and concurrently evaluated for phenotype traits and phaseolin patterns. A total of 140 alleles were detected with an average of 4.67 per locus. The polymorphic information content ranged from 0.215 to 0.823, with an average of 0.488. Nei's genetic distances between accessions ranged from 0 to 0.9999, with an average of 0.6143. In those Chinese snap beans, structure analysis proved the existence of a high proportion of hybrid accessions except for identification of Andean and Mesoamerican gene pools. Neighbor‐joining clustering and principal coordinate analysis based microsatellite markers were similar in explaining the extent of diversity with both revealed Andean and Mesoamerican gene pools, which were divided into seven subgroups. Four of those subgroups, including one arising from introgression, were identified as belonging to the Andean gene pool, which likely represented Nueva Granada and Peru races. Other three subgroups were identified as belonging to the Mesoamerican gene pool, which likely represented the Mesoamerican race, owing to their close association with the control genotype. The diversity index of the qualitative traits was 0.80 to 1.88, with the average value of 1.20, while the diversity of the quantitative traits was ranked as 100‐seed weight (H′ = 1.98) > pod length (H′ = 1.90). Six principal components explained 69.13% of the total variation. Eight phaseolin patterns were identified in the 221 accessions. This study demonstrated the gene pool, as well as geographical, diversity of snap bean germplasms in China. The substantial diversity level is important for the utilization and conservation of snap bean, as well as future breeding programs. Core Ideas: The distinction in snap bean of China has blurred between Andean and Mesoamerican pools for obvious introgression.The combination of microsatellites, phaseolin, and phenotypic traits is effectively evaluated for genetic diversity.Phaseolin can separate two gene pools but not be well detected population structure and new variation. [ABSTRACT FROM AUTHOR]