Aedes (Stegomyia) albopictus (Skuse) is a major global invasive mosquito species that, in Japan, co-occurs with Aedes (Stegomyia) flavopictus Yamada, a closely related species recently intercepted in Europe. Here, we present results of a detailed 25-month long study where we biweekly sampled pupae and fourth instar larvae of these two species from ovitraps set along Mt. Konpira, Nagasaki, Japan. This setting allowed us to ask whether these species had different responses to changes in environmental variables along the altitudinal gradient of an urban hill. We found that spatially Ae. albopictus abundance decreased, while Ae. flavopictus abundance increased, the further away from urban land. Ae. flavopictus also was more abundant than Ae. albopictus in locations with homogenous vegetation growth with a high mean Enhanced Vegetation Index (EVI), platykurtic EVI, and low SD in canopy cover, while Ae. albopictus was more abundant than Ae. flavopictus in areas with more variable (high SD) canopy cover. Moreover, Ae. flavopictus abundance negatively impacted the spatial abundance of Ae. albopictus. Temporally we found that Ae. flavopictus was more likely to be present in Mt. Konpira at lower temperatures than Ae. albopictus. Our results suggest that spatial and temporal abundance patterns of these two mosquito species are partially driven by their different response to environmental factors.