By using genetic engineering to improve yeast strains, it is often necessary to distinguish the transformants obtained. The purpose of the study was to compile a RAPD-PCR assay with four microsatellite primers: (GTG)₅ , (GAC)₅ , (GACA)₄ and M13, and phylogenetic analysis for differentiation of yeast strains Yarrowia lipolytica obtained by homologous or heterologous transformation with a transgenic SUC2 from Saccharomyces cerevisiae under the control of the XPR2 promoter and flanked by URA3 gene fragments from Y.lipolytica. For several transformants, the presence of the SUC2 gene was confirmed by PCR with specific primers and hybridization probe. The phylogenetic analysis of 20 strains was performed on the basis of a dendrogram, prepared with similarity matrices obtained from RAPD-PCR results. The applied technique with one exception enabled the homologous and heterologous transformants to be grouped into two separate clusters with 79% of similarity. The first group included the parent strain Y.lipolytica A-101 and 10 of 11 Suc⁺Ura⁺ clones (B56-5, B60-4, B14-6, B10A-5, B7-6, B59-3, KLON1, KLON10, B58-2, B61-5). The second group (except for strain B62-1 with Suc⁺ Ura⁺ phenotype) included clones B1-1, B9-2, A50 presented Suc^-Uraphenotype.

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