Thermoduric bacteria are heat-resistant microorganisms capable of surviving pasteurization, making them persistent challenges in dairy safety and quality. This study aimed to characterize thermoduric bacteria present in raw milk using two enumeration methods - Laboratory Pasteurization Count (LPC) and modified Laboratory Pasteurization Count (mLPC) - followed by molecular identification through PCR amplification and 16S rRNA gene sequencing. Bacterial isolates obtained from both methods were compared to assess diversity and detection efficiency. Over 1,100 isolates were recovered and identified, with Bacillus emerging as the most dominant genus. The mLPC method captured a broader range of both spore forming and non-spore forming genera compared to LPC, indicating its improved sensitivity. These findings underscore how method selection influences bacterial recovery and highlight the value of integrating classical and molecular approaches. This study contributes to a better understanding of raw milk’s microbial ecology and informs improved monitoring strategies for thermoduric organisms in the dairy industry.