Maar Lake is a unique type of lake in geological structures, and little is known about microbial diversity in various Maar Lakes worldwide. In order to understand the community structures of culturable bacteria in Huguangyan Lake, a typical Maar lake in South China, BOX-PCR was introduced as a screening technique for bacterial isolates that were obtained from three water depths in winter and summer through the general R2A plates and in situ lake-water agar medium. The results indicated that the changes of bacterial abundance were consistent along water column and on the two types of medium: 5 m>1 m>13 m for summer and 1 m>5 m>13 m for winter, with Proteobacteria as the dominant bacteria followed by Actinobacteria, Firmicutes, and Bacteroides. BOX-PCR profiles for cultured bacteria on both mediums were similar, but their community structures were not identical. The bacterial diversity was higher in winter than that in summer, in consistent with the trends found in other similar primitive lakes. Our results show that using different media may have different limitations in cultivating microbes from natural environments. This study may contribute to the understanding of significant relationship between microbial diversity and environmental characteristics in unique Maar Lakes and to the isolation of novel functional bacteria.