Habitat heterogeneity has been shown to promote co-existence of closely related species. Based on this concept, a field study was conducted on the niche partitioning of three territorial congeneric species of skimmers (Anisoptera: Libellulidae) in Northeast Algeria during the breeding season of 2011. According to their size, there is a descending hierarchy between Orthetrum nitidinerve Sélys, O. chrysostigma (Burmeister), and O. coerulescens anceps (Schneider). After being marked and surveyed, the two latter species had the same breeding behavior sequence. Knowing that they had almost the same size, such species could not co-occur in the same habitat according to the competitive exclusion principle. The spatial distribution of the three species was investigated at two different microhabitats, and it was found that these two species were actually isolated at this scale. O. chrysostigma and O. nitidinerve preferred open areas, while O. c. anceps occurred in highly vegetated waters. This study highlights the role of microhabitat in community structure as an important niche axis that maintains closely related species in the same habitat.