Microbiota refers to a colony of microorganisms, and they are found in all multicellular organisms. This colony plays a major role in both the physiology and disease of the organism it inhabits. Much attention has been paid to host-microbiota interactions, but there has been little investigation on its role in carcinogenesis. In this study, we characterized a fecal mycobiota, also known as fungal signature, for the first time with 131 subjects, comprising polyp and colorectal cancer (CRC) patients, as well as a healthy control population. The data obtained were analyzed to assess the biodiversity and composition of the fungi. The impacts of anatomic position and tumor stage on the mycobiota were also evaluated. Correlations between fungi were investigated using the Spearman test. We observed fungal dysbiosis in colon polyps and CRC, including decreased diversity in polyp patients, an increased Ascomycota/Basidiomycota ratio, and an increased proportion of opportunistic fungi Trichosporon and Malassezia, which might favor the progression of CRC. Subsequent analysis with regard to tumor stage demonstrated a lower diversity and significant mycobiota alteration in early-stage tumors. Finally, the fungal correlation showed a close relationship within the community and concomitantly revealed a dramatically structured discrepancy in each clinical phenotype. In conclusion, our study has uncovered a distinct fungal dysbiosis and an alteration in the fungal network, which could play important roles in polyp and CRC pathogenesis.