Inter-Simple Sequence Repeat (ISSR) and Randomly Amplified Polymorphic DNA ( RAPD) markers were used to analyze genetic distance among H. vulgare subsp. spontaneum populations from west Turkey. Fifty-five RAPD and 10 ISSR primers were used to detect variation among sample. A total of 55 polymorphic loci were found using 65 primers. Two distinct cluster groups were clearly established among populations. The minimum variation was detected between Pinarbasi and Bornova ( GD = 0.192) populations and the maximum was found between Icmeler and Aydin populations ( GD = 0.926). As two dominant markers, RAPD and ISSRs are effective and promising marker systems for detecting genetic variation.