Lotic systems are rapidly changing due to anthropogenic impacts, making it crucial to note the diversity and abundance of Odonates for effective conservation of these running waters. Our study aimed to assess and compare the Odonate communities in two adjacent rivers, Medjerda and Cheref, in Souk Ahras, northeastern Algeria collected during the period from January 2022 to August 2023. In total, 27 species belonging to 7 families and 17 genera were recorded, with three rare species in Numidia, and three Maghrebian endemic species, including Gomphus lucasii (Selys, 1850) listed as "Vulnerable" in the IUCN Mediterranean Red List. Coenagrion mercuriale (Charpentier, 1840), a locally endangered species, was abundantly present in the Medjerda River. Additionally, the presence of the desert species Trithemis kirbyi (Selys, 1891) in Medjerda confirms their northward expansion within Algeria. The Libellulidae were the most dominant family with 11 species. Our findings revealed no significant differences in terms of biodiversity indices (Richness, Simpson, Shannon, & Pielou's evenness) between the two rivers. However, significant dissimilarities were observed in Odonate assemblages likely due to habitat and environmental variations. Many factors, such as water pumping, overgrazing, untreated wastewater, and riverbank development, which influence Odonate species, were observed in the two rivers. Consequently, an urgent conservation plan should be put in place to preserve water resources and biodiversity in the region. This study highlights the need for continued monitoring and conservation efforts, especially for rare and threatened species in the face of increasing anthropogenic pressures on these aquatic ecosystems.