As a sub-project under the frame of the Third National-Wide Investigation of Crop Germplasm Resources Project in China, we conducted the survey and collection of 76 cowpea germplasms in 32 counties in Zhejiang Province, followed by the morphological diversity analysis at 44 agronomic traits in the field trials. Out of 76 accessions, 30 asparagus bean accessions (V. unguiculata ssp. sesquipedialis) and 46 common cowpea accessions (V. unguiculata ssp. unguiculata) have been identified. The large genetic variation on the growth habits, fresh pod characters and yield-related traits in this collection have been observed. Moreover, these accessions were subjected for a genotyping with 101 SNP markers. PCA and phylogenetic tree analysis showed two sub-populations (long-podded vs. short-podded) based on the pod length. The asparagus bean accessions are often detected in the long-podded subpopulation, while common cowpea accessions were predominant in the short-podded subpopulation. Collectively, our results unlocked the genetic diversity of Chinese cowpea germplasms collected from Zhejiang province, which might be valuable resources in the exploration of local cowpea resources and in breeding for new cultivars.