Background: Members of the phylum Verrucomicrobia, especially Akkermensiamuciniphila, have been identified as beneficial gut bacteria. Changes in the gut microbiota are associated with the occurrence of metabolic diseases, such as diabetes, obesity, and irritable bowel syndrome; however, there is conflicting information about their role and changes in colorectal cancer (CRC). Objectives: In the present study, the prevalence of this bacterial phylum in the intestines of individuals with colorectal lesions and healthy controls was investigated. Methods: Mucus samples were obtained from the colons of 69 individuals with colorectal lesions, including CRC and precancerous gut lesions (PCL), and 68 individuals without lesions during colonoscopy. Bacterial DNA was extracted from the mucus samples. A conventional polymerase chain reaction (PCR) assay was performed to detect Verrucomicrobia using a specific 16S rRNA primer. Results: The prevalence of Verrucomicrobia was greater in healthy individuals (75.4%) than in those with either cancer or PCL (59.7%) (P = 0.038). However, there was no significant difference in the presence of these bacteria between the CRC and PCL patient groups. A reverse correlation was observed between the presence of Verrucomicrobia and both chronic constipation (P = 0.001) and anemia (P = 0.048). Conclusions: A decreased frequency of Verrucomicrobia in humans may serve as the basis for the initiation of intestinal changes, resulting in the development of colorectal precancerous and cancerous lesions.