The aim of this study was to determine distribution of the Candida (C.) species in onychomycosis and analyses in vitro susceptibility to fluconazole and itraconazole. In recent years, cases of onychomycosis in Lithuania caused by Candida have increased significantly. In the period between 2009 and 2016, a total of 8149 clinical cases (outpatients and inpatients) were investigated at the Vilnius University Hospital Santaros Clinics (VUH SC). Candida yeasts were identified using VITEK 2 (BioMerieux, France) and IVD Maldi biotyper 2.3 (Bruker Daltonik GmbH, Germany), automated systems for identification of yeasts. The antifungal susceptibility to the Candida species were determined by disc diffusion. Candida spp. were the most frequently isolated pathogens in onychomycosis during the investigation period. The main species in onychomycosis were C. albicans (38.6%), followed by C. krusei (33.7%), C. tropicalis (11.1%), C. parapsilosis (7.9%), and other Candida (8.7%). The different antifungal susceptibility patterns among Candida species confirm the need to perform antifungal susceptibility in vitro testing of yeasts from patients with onychomycosis.