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Abstract Background Colorectal cancer (CRC) has been regarded as one of the most frequently diagnosed malignancies among the leading causes of cancer-related morbidity and mortality globally. Diagnosis of CRC at the early-stages of tumour might improve the survival rate of patients. The current study sought to determine the performance of fecal Fusobacterium nucleatum (F. nucleatum) and Streptococcus bovis (S. bovis) for timely predicting CRC. Methods Through a case–control study, the fecal sample information of 83 individuals (38 females, 45 males) referring to a hospital in Tehran, Iran was used. All patients underwent a complete colonoscopy, regarded as a gold standard test. Bacterial species including S. bovis and F. nucleatum were measured by absolute quantitative real-time PCR. The Bayesian univariate and bivariate latent class models (LCMs) were applied to estimate the ability of the candidate bacterial markers in order to early detection of patients with CRC. Results Bayesian univariate LCMs demonstrated that the sensitivities of S. bovis and F. nucleatum were estimated to be 86% [95% credible interval (CrI) 0.82–0.91] and 82% (95% CrI 0.75–0.88); while specificities were 84% (95% CrI 0.78–0.89) and 80% (95% CrI 0.73–0.87), respectively. Moreover, the area under the receiver operating characteristic curves (AUCs) were 0.88 (95% CrI 0.83–0.94) and 0.80 (95% CrI 0.73–0.85) respectively for S. bovis and F. nucleatum. Based on the Bayesian bivariate LCMs, the sensitivities of S. bovis and F. nucleatum were calculated as 93% (95% CrI 0.84–0.98) and 90% (95% CrI 0.85–0.97), the specificities were 88% (95% CrI 0.78–0.93) and 87% (95% CrI 0.79–0.94); and the AUCs were 0.91 (95% CrI 0.83–0.99) and 0.88(95% CrI 0.81–0.96), respectively. Conclusions Our data has identified that according to the Bayesian bivariate LCM, S. bovis and F. nucleatum had a more significant predictive accuracy compared with the univariate model. In summary, these intestinal bacteria have been highlighted as novel tools for early-stage CRC diagnosis.