Introduction: Candida is a normal flora of the oral cavity, gastrointestinal tract (GIT) and the vagina but has been reported to become opportunistic pathogen (switch) in certain disease conditions. An investigation into this switch in the GIT will give a clear insight into their progression from commensal to opportunistic pathogens. Therefore, this study aimed to isolate and evaluate the presence of Candida species and associated microbes causing GIT infections among patients accessing care at a tertiary healthcare facility in Lagos, southwest Nigeria Methodology: A total of 150 consenting participants (M=82; F=68) age ranged 1-60 years were recruited into this study between July and December 2019 at the Lagos University Teaching Hospital, Idi-araba using standard methods. Demographic details were taken and characte¬ristics of the stool specimens were noted. Samples were examined macroscopically and microscopically, then cultured on Sabouraud dextrose agar with corn meal extract along with other bacteria culture media and incubated appropriately. CHROMagar TM for Candida was used for presumptive identification of isolates and was further confirmed with the API32C system for Candida.Results: An overall rate for Candidiasis in this study was 26.7% (40/150) with female having higher rate 18.7% (28/150) than 14.7% in male (22/150). Twenty-five (16.7%) of the participants' stool culture yielded pure fungi isolates of C. albicans. As for C. albicans, the female had higher rate (10%) than their male (6.7%) counterparts. However, by gender, this was not statistically significant (p=0.012). Pathogenic stool bacteria isolates were found in 16 (10.7%) and 84 (56%) of participants with normal flora of the GIT. The remaining 25 (16.7%) were reported as mixed culture of Candida spp. Also, C. albicans and C. dubliniensis were found as a pair in seven stool samples from participants with cases of peptic ulcer disease 1(14.3%), gastrointestinal bleeding 4(57.1%)), immune suppression 2(28.6%) while others occurred in combinations of threes and fours of different species. Obvious clinical manifestations when compared with the study findings revealed that C. albicans co-existed as the causative fungi causing gastroenteritis in 17% of the participants whose stool culture yielded pure growth. Conclusion:This study found comparable high burden of Candida isolates and associated GIT microbes. Although the rates were higher in female than their male counterparts, these findings were however not statistically significant, this therefore calls for better hygiene practice through educative advocacy. Effective management of opportunistic mycoses depends on identification of the specific organism causing the infection otherwise, a systemic infection of this type can be fatal.