Introduction: This study aimed to differentiate among the species belonging to the Candida parapsilosis complex, which is one of the leading causes of systemic mycoses through molecular characterisation and to determine their antifungal resistance pattern. Material and Methods: Ninety-five C. parapsilosis complex isolates identified using two yeast identification systems, BioMérieux ID 32C and Vitek 2™ with YST card, were included in this study. Molecular characterisation was achieved by polymerase chain reaction–restriction fragment length polymorphism analysis of the secondary alcohol dehydrogenase gene. Isolates that could not be identified using this technique were identified by internal transcribed spacer (ITS) sequencing. Antifungal susceptibility was evaluated using the Vitek 2™ AST-YS06 card. Results: Out of the 95 isolates, 94 were identified as C. parapsilosis sensu stricto, and only one isolate was identified as C. orthopsilosis; the latter result was achieved using ITS sequencing. C. orthopsilosis was susceptible against all tested antifungal agents. Among the C. parapsilosis sensu stricto isolates, three were found to be resistant: one to amphotericin B, two to fluconazole of which one showed intermediate resistance to voriconazole. Discussion: Isolation rates of C. orthopsilosis and C. metapsilosis in this study show that they are rare species. It was not possible to compare resistance among these three species due to very low isolation rates of C. orthopsilosis and C. metapsilosis. The use of molecular identification tests for these species in routine laboratory settings remains controversial. Nevertheless, their isolation rates and antifungal resistance patterns are important from the epidemiological viewpoint.