This study aimed to evaluate the appropriateness of MRS-C (0.05% L-cystein; pH 5) and BHI-CM (0.05% L-cystein, 0.5% mucin) agars for the selective isolation of bifidobacteria in fecal samples compared to blood-liver-NPNL (BL-NPNL) agar. Over 200 isolated colonies were characterized morphologically and biochemically. Genomic DNA was extracted from pure cultures of the isolated strains, followed by PCR amplification of the 16S rRNA gene. Bifidobacterium longum and B. animalis were selectively isolated from MRS-C agar and Lactobacillus acidophilus and Enterococcus avium were also isolated. B. longum, B. faecale, and B. animalis were isolated from feces on BHI-CM agar; however, different Bacteroides strains (including Bac. fragilis, Bac. kiribbi, Bac. ovatus, Bac. koreensis, and Bac. salyersiae) were also detected. BL-NPNL agar successfully isolated B. longum and Bacillus, while other Bifidobacterium and Bacteroides species could not grow owing to the presence of antibiotics in the medium. The use of antibiotics in a medium can enhance the selectivity; however, antibiotics may inhibit the growth of certain bacteria in a sample. Hence, adjusting pH or adding non-antibiotic nutrients to the medium is more advantageous, than relying on antibiotics.