Thermotolerant non-albicans Candida (NAC) species among immunocompromised patients pose a significant threat to public health. These species, including the multidrug-resistant C. auris, can thrive at high temperatures and survive NaCl2 concentration, allowing them to colonize and infect human skin. This study aimed to isolate and identify thermotolerant non-albicans Candida species from diabetic and malignant patients in Jos, Nigeria, and to determine the possible risk factors associated with candidiasis among the participants. A total of 702 samples, from the armpit and inguinal fold of the groin of patients, were inoculated on Sabouraud dextrose agar (SDA) containing chloramphenicol (250 mg/L), sub-cultured on three selective media, and incubated at 42 °C for 48 hours. Halotolerant and thermotolerant tests were conducted using a 10-fold serial dilution method. Twenty-three-point nine percent (23.9%) of patients tested positive, with Candida glabrata (12.5%) being the predominant species, followed by Candida tropicalis (5.1%), suspected C. auris (2.3%), and C. krusei and C. parapsilopsis, each at 1.4%. Some patients experienced co-infections. Identified risk factors included cardiovascular complications, prolonged use of antibiotics, immunosuppressive therapy, and catheterization. This study highlights the pathogenic thermotolerant non-albicans Candida species as a critical consideration for diagnostic processes to facilitate isolation, particularly among patients with diabetes and malignancy.