The aim of this study was to compare culture-dependent and -independent methods in microbial community analysis with a focus on post-mortem microbiomes, particularly in forensic contexts. By utilizing full-length 16S rRNA gene sequencing and propidium monoazide (PMA) treatment, we identified a broader range of microorganisms than that identified using the traditional culture-dependent method. The inclusion of long-read sequencing further enhanced species resolution, addressing limitations associated with short-read sequencing of the V3-V4 region. PMA-treated samples exhibited a higher microbial diversity, indicating the advantages of culture-independent approaches in forensic microbial analysis. Moreover, beta-diversity analysis demonstrated slight differences in microbial composition before and after PMA treatment, but the overall community structure remained similar. Our approach revealed a distinct shift in microbial communities when comparing culture-dependent and -independent methods, with culture-independent approaches yielding richer microbial diversity. These findings emphasize the necessity of culture-independent methods and the use of PMA in forensic microbiology for more accurate microbial profiling and improved forensic applications. The study underscores the value of combining these methodologies to better understand microbial dynamics in post-mortem samples, advancing forensic science.