Apple is among the most widely grown fruit species worldwide. It is included in the genus Malus and there are several species of apple. Although a consensus is not available about the origin of domesticated apples, it is widely accepted that Malus sieversii, known as Central Asia wild apple, was the primary progenitor of apples. Central Asia is a quite significant origin center of apple and harbors different species and a great diversity. In this study, genetic relations among 79 apple materials belonging to 4 different species (M. domestica, M. sieversii, M. kirghisorum and M. niedzwetzkyana) collected from different regions of Kyrgyzstan, Central Asia and their population structures were put forth. A total of 15 ISSR markers were used and 79 bands were obtained with a polymorphism ratio of 75.2%.