Most genetic markers carry numerous limitations which question their credibility. Ribosome protein Exon Primed Intron Crossing (Rp EPIC) markers claimed to eff ectively overcome some of these limitations. Hence, the present study was aimed at demonstrating the scope of Rp EPIC markers in population genetics in comparison to conventional microsatellites, using the dengue vectors; Aedes aegypti and Aedes albopictus. A total of 62 Ae. aegypti and 51 Ae. albopictus samples were genotyped for two Rp EPIC markers; RpS20b and RpL30a and two microsatellite markers; AC7 and BbH08 for Ae. aegypti and Alb-tri 03 & Alb-tri 25 for Ae. albopictus. The Rp EPIC markers were successfully transferred among the two species, while diff erentiating them based on F statistics. Total size variants (electromorphs) observed for the two markers, RpS20b and RpL30a were 14 (3 for Ae. aegypti; 13 for Ae. albopictus; shared: 2) and 7 (3 for Ae. aegypti; 4 for Ae. albopictus; shared: 0) with many more alleles uncovered through sequencing (RpS20b:74 and RpL30a:54). In contrast, microsatellites produced 6 (AC7) and 3 (BbH08) size variants for Ae. aegypti and 8 (Alb-tri 03) and 7 (Alb-tri 25) for Ae. albopictus. Both marker types detected genetic structure among Ae. albopictus populations while a genetic structure among Ae. aegypti was detected only with microsatellites and not with Rp EPIC size variants. The combined data of microsatellites and Rp EPIC size variants as well as sequence analysis did not support the presence of a genetic structure among the studied Ae. aegypti populations. It is possible that microsatellites tend to infl ate genetic diff erentiation among the studied Ae. aegypti populations, which has been counteracted by the Rp EPIC markers.