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Our objective was to investigate the effects of different delivery and feeding modes on the gut microbiota composition of early infants with special emphasis on <i>Bifidobacterium</i> and <i>Lactobacillus</i> profiles at species level. 16S rRNA V3-V4 regions, bifidobacterial, and lactobacilli <i>groEL</i> genes from infant feces were sequenced by Illumina MiSeq. Gut microbiota abundance was significantly different, where standard vaginally delivered (SVD) and breast-fed (BF) groups were higher in comparison with caesarean section (CS), milk-powder-fed (MPF), and mixed-fed (MF) groups. The genus unclassified Enterobacteriaceae was dominant, followed by <i>Bifidobacterium</i>, which was highly abundant in SVD and BF groups. The dominant <i>Bifidobacterium</i> species in all groups were <i>B. longum subsp. longum</i>, <i>B. longum subsp. infantis</i> and <i>B. animalis subsp. lactis</i>. <i>B. dentium</i> and the diversity of <i>Bifidobacterium</i> in SVD and BF groups were significantly higher. For <i>Lactobacillus</i> profiles, <i>L. rhamnosus</i> and <i>L. gasseri</i> were dominant among all the groups, while <i>Lactobacillus</i> species in CS and MPF groups were more diverse. Functional predictions showed significant differences between delivery mode and feeding groups, such as phosphotransferase system as well as taurine and hypotaurine metabolism. In early infants with different delivery and feeding methods, gut microbiota&#8212;particularly bifidobacteria and lactobacilli communities&#8212;showed significant differences, with strong implications for physiological functions.