The Zhejiang Team of the Third Nation-wide Survey and Collection of Agricultural Crop Germplasm Resources Project newly collected a total of 51 accessions of local germplasm resources of bottle gourd [Lagenaria siceraria (Mol.) Stand.]. In this study, these accessions were grown and evaluated in the field, with 15 main agronomic traits investigated. The results showed that they were richly varied in many agronomic traits, and through cluster analysis were divided into three groups, among which group I showed excellent comprehensive agronomic properties and could be developed and utilized directly or indirectly. The genotypes of the accessions were identified using 22 core SNP markers, and cluster analysis of the genetic diversity and population structure of these local germplasm resources revealed that they were divided into two groups mainly related to geographical distributions. A comprehensive comparison of the two methods of germplasm clustering analysis showed that it was more accurate and objective to use the molecular marker method to distinguish germplasm resources, when the two methods were not identical. Our results provided a theoretical basis for further research and utilization of these bottle gourd local germplasm resources.