Objectives: Aedes aegypti and Ae. albopictus transmit several medically important arboviruses to humans. These mosquitoes can carry gregarine protozoan parasites that invade the midgut epithelial cells, where they complete their life cycles. There are no reports of the presence of this parasite associated with Aedes species in Ecuador. This study aimed to identify the presence of Ascogregarina in naturally infected Ae. aegypti and Ae. albopictus that were collected in several localities of Ecuador. Methods: The Ascogregarine parasite was identified morphologically by microscopy and by sequencing using a ssrRNA conserved region. Results: We present the first record of the protozoan Ascogregarina culicis infecting Aedes aegypti from Ecuador. The parasite was found in 30 adult and immature mosquitoes out of 260 individuals. Conclusion: This study presents tools to identify the parasite and highlights the importance of studying the parasitism of mosquitoes for biological control and their possible role in arbovirus transmission.