Forty two Candida albicans isolates were collected from clinical samples in Israel. Twenty strains were isolated from blood cultures and 22 from superficial candidiasis. Isolates were typed by MLST analysis. Thirty-seven Diploid Sequence Types (DSTs) were identified. Seventeen isolates (40.5%) displayed new DSTs; 34 (81%) clustered within previously described clades, while nine (19%) did not cluster in any known group. Clonal Complex (CC) 124 was the most prevalent in both candidemia and superficial candidiasis isolates, CC 918 was only found in candidemia strains. To the best of our knowledge, this is the first study analyzing C. albicans clinical isolates from Israel using MLST methodology, possibly pointing to geographic differences in strain distribution.