Weeds are one of the most important factors affecting yield and quality in cotton production. Firstly, all the problematic weed species and their densities should be determined in successful weed control. This study aims to identify the weed species that pose a problem in the cotton production areas of Siirt and Batman, located in the Southeastern Anatolia region, as well as to determine their prevalence and density. Survey studies in the study area were carried out in a total of 39 cotton fields in 2021 and 2022 cotton growing seasons. Total of 40 weed species belonging to 16 families were identified in the study. The most common species recorded in Siirt province were Cyperus rotundus L. (%100), Xanthium strumarium L. (%93), Sorghum halepense var. halepense (L.) Pers. (%93), Portulaca oleracea L. (%93) and Physalis spp. (%86). The most common species in Batman province were Amaranthus retroflexus (%100), Physalis spp (%93), Echinochloa colonum (%86), Portulaca oleracea (%80) and Sorghum halepense (%80). The species identified in the study area are similar to the species common in cotton cultivation areas in Turkey, but significant differences were detected in the prevalence and density of the species. It indicates that agricultural irrigation in the region will increase, and the fertilization and soil management strategies will differ in the near future, and the herbicides use in weed control and the weed composition will also change depending on the climate change. Therefore, continuous monitoring and observations are needed for early intervention in the region.