Odonate nymphs are important predators of the immature aquatic stages of mosquitoes. Populations of the malaria vector Anopheles pseudopunctipennis Theobald (Diptera: Culicidae) can be efficiently reduced by extraction of filamentous algae from river pools in southern Mexico. Here, we examined the influence of this intervention on the diversity of odonates associated with mosquito breeding pools after annual extractions of algae from river pools in a 3-km section of the Coatán River, over a period of 2 yr. Odonate sampling was performed at monthly intervals in control and treated sections of the river for 4–5 mo after extraction in both years and before extraction in 1 yr. In total, 16 species, 10 genera, and 6 families of odonates were collected. Shannon diversity index values declined significantly during a period of 1 mo in 2001 and >5 mo in 2002. However, the abundance of odonates captured was not affected by algal extraction. In contrast, year-to-year variation in the diversity and abundance of the odonate community was strongly influenced by precipitation and river volume. Despite the importance of algae in river ecology, we conclude that the mosquito control intervention resulted in minimal impact on the odonate community in southern Mexico.