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¹ Biology Department, Middle East Technical University, Ankara, Turkey DOI : 10.51458/BSTD.2021.8 Viewed : 3208 - Downloaded : 1285 Potential of Inter Simple Sequence Repeats (ISSR) markers in analyzing and discriminating of Turkish honeybee populations was assessed in this study. Genomic DNA samples of workers belonging to four subspecies and two ecotypes of honey bees were amplified by PCR using 5 microsatellite primers. Principal component and population structure analyses showed that ISSR method successfully defined and discriminated four distinct Turkish honeybee subspecies while the two ecotypes of Anatoliaca subspecies were not distinctively separated from each other. This study showed that ISSR markers can be a simple and low-cost alternative with high resolution compared to other markers such as microsatellite and RAPD, in analyzing the genetic variations in Turkish honey bee subspecies. Keywords : Inter simple sequence repeats Genetic diversity Subspecies distinction