Caves are semi-closed ecosystems that experience the absence of sunlight and often, poor organic matter conditions due to physical isolation. Therefore, microbial activity is a crucial factor for sustaining life in caves. However, the heterogeneity of microbial diversity and community structure in relation to different types of habitats in karstic caves (e.g., drip water residue, mineral deposits, rock varnish) remains largely unknown. In this study, cave deposit samples in various morphology were analyzed to reveal its bacterial and archaeal diversity of Insuyu Cave in Burdur Province that is located in central Turkey. Illumina MiSeq sequencing of seven cave deposit samples (S1-S7) from the zones with a diverse array of environmental conditions revealed a total of four bacterial phyla including (1) Proteobacteria ranging from 80.20% to 98.72%, (2) Actinobacteria ranging from 0.23-13.03%, (3) Firmicutes ranging from 0.18 to 12.61% and (4) Bacteroidetes ranging from 0.00% to 3.80%, while none of the samples exhibits sign for archaeal life form. The heatmap diagram on abundance and distribution of the genera, referring to the results of 16S rRNA gene-based metagenomic analysis of the cave-dwelling microbial communities in Insuyu Cave, revealed that the structures of the bacterial communities were significantly different across the samples (S1-S7). The high abundance of taxa that is relevant to anthropogenic activity revealed a strong impact of agricultural activity on the bacterial composition of Insuyu Cave.