Background: Efficient bioconversion of organic waste requires microorganisms with the potential to degrade complex organic compounds and transform biogenic elements. Methods: In this study, two thermophilic bacterial strains, RKM-1 and RKM-2, isolated from sewage sludge, were characterized using whole-genome sequencing and comparative genomics to establish their taxonomic positions and assess their functional potential. Results: RKM-1 and RKM-2 were identified as Bacillus subtilis and Bacillus licheniformis, respectively, with maximum ANI values of 98.76% and 99.76%. Comparative genomic analysis revealed differences in the functional potential of the two strains. RKM-1 exhibited genomic features associated with the transformation of biogenic elements and secondary metabolite biosynthesis, whereas RKM-2 showed greater genetic potential for the utilization and transformation of complex carbohydrates, supported by the presence of genes such as amyA, bglC, celA, glcT, galE, galU, and glgABCD. These differences indicate potentially complementary functional profiles of the two strains in the bioconversion of organic substrates. During sewage sludge composting, inoculation with both strains accelerated the onset of the thermophilic phase. Bacillus subtilis RKM-1 reached the highest compost temperature (60 °C), whereas Bacillus licheniformis RKM-2 most effectively promoted compost maturation, reducing the C:N ratio to 9:1 within 60 days. Conclusions: These findings demonstrate a strong relationship between the genomic characteristics and functional traits of the investigated strains and highlight the value of comparative genomics as a powerful tool for identifying promising thermophilic microorganisms for efficient bioconversion of organic wastes.