The aim of the present cohort study was to compare oral carriage of Candida in waterpipe smokers (WS), cigarette smokers (CS), and non-smokers (NS). A total of 141 individuals (46 WS, 45 CS, and 50 NS) were included. A questionnaire was used to gather demographic information and data on the daily frequency and duration of smoking habits, the reasons for smoking, and daily oral hygiene maintenance habits. Oral Candida (C.) samples were cultured and yeast species were identified using polymerase chain reaction. Unstimulated whole salivary flow rate (UWSFR) was also recorded. The numbers of missing teeth (MT) were counted and tongue lesions were clinically identified. C. albicans was the most prevalent yeast species isolated from all groups. Oral C. albicans carriage was higher among WS (P < 0.05) and CS (P < 0.05) than among NS. Oral C. tropicalis carriage, age, UWSFR and the number of MT were comparable among the groups. Oral Candida carriage was significantly higher among WS and CS than among NS. Therefore it appears that WS and CS are at an increased risk of developing oral candida infections.