Since the beginning of rice cultivation, weed control has been a problem in Türkiye as well as in many other countries. Rice has both an important cultural plant and limited production for Türkiye. There are significant yield losses due to weeds and therefore weed control has an important place in rice agriculture. Species belonging to the genus Scirpus in rice production areas have recently become an important problem in rice cultivation areas of Türkiye as well as in rice cultivation areas of many other countries. In order to determine the morphological and genetic diversity of Scirpus mucronata, which is a problem in rice cultivation areas in Türkiye, 62 populations collected from the rice production areas of the Marmara and Black Sea Regions were evaluated over 8 ISSR primers and 12 morphological parameters. In the ISSR study, observed and expected heterozygosity levels ranged from 0.192 to 0.970 and from 0.136 to 0.566, respectively. In the morphological and molecular analyses performed, differences were detected in some quantitative characters between the examined populations. While morphological similarities were found between the populations grown in different regions that could not be ignored, genetic diversity was found to be higher. Morphological and genetic relationships between populations were not found to be related to geographic distance. In the context of the results, it is important to focus on field management practices such as cultural methods, as well as good control of rice seed traffic and herbicide use. It should not be forgotten that these measures are important in terms of integrated weed management strategies.