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We investigated associations of habitual dietary intake with the taxonomic composition and diversity of the human gut microbiota in 222 Koreans aged 18–58 years in a cross-sectional study. Gut microbiota data were obtained by 16S rRNA gene sequencing on DNA extracted from fecal samples. The habitual diet for the previous year was assessed by a food frequency questionnaire. After multivariable adjustment, intake of several food groups including vegetables, fermented legumes, legumes, dairy products, processed meat, and non-alcoholic beverages were associated with major phyla of the gut microbiota. A dietary pattern related to higher α-diversity (HiαDP) derived by reduced rank regression was characterized by higher intakes of fermented legumes, vegetables, seaweeds, and nuts/seeds and lower intakes of non-alcoholic beverages. The HiαDP was positively associated with several genera of <i>Firmicutes</i> such as <i>Lactobacillus</i>, <i>Ruminococcus</i>, and <i>Eubacterium</i> (all <i>p</i> < 0.05). Among enterotypes identified by principal coordinate analysis based on the β-diversity, the <i>Ruminococcus</i> enterotype had higher HiαDP scores and was strongly positively associated with intakes of vegetables, seaweeds, and nuts/seeds, compared to the two other enterotypes. We conclude that a plant- and fermented food-based diet was positively associated with some genera of <i>Firmicutes</i> (e.g., <i>Lactobacillus</i>, <i>Ruminococcus</i>, and <i>Eubacterium</i>) reflecting better gut microbial health.