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Novel approaches to suppress dengue and other mosquito-borne diseases involve changing the composition of mosquito vector populations, particularly through Wolbachia endosymbionts. The success of these strategies depends on understanding the dynamics of vector populations. In preparation for Wolbachia releases around Yogyakarta, we have studied Aedes populations in five hamlets. Adult monitoring with BioGent-Sentinel (BG-S) traps indicated that hamlet populations had different dynamics across the year; while there was an increase in Aedes aegypti (L.) and Aedes albopictus (Skuse) numbers in the wet season, species abundance remained relatively stable in some hamlets but changed markedly (>2 fold) in others. Local rainfall a month prior to monitoring partly predicted numbers of Ae. aegypti but not Ae. albopictus. Site differences in population size indicated by BG-S traps were also evident in ovitrap data. Egg or larval collections with ovitraps repeated at the same location suggested spatial autocorrelation (<250 m) in the areas of the hamlets where Ae. aegypti numbers were high. Overall, there was a weak negative association (r < −0.43) between Ae. aegypti and Ae. albopictus numbers in ovitraps when averaged across collections. Ae. albopictus numbers in ovitraps and BG-S traps were positively correlated with vegetation around areas where traps were placed, while Ae. aegypti were negatively correlated with this feature. These data inform intervention strategies by defining periods when mosquito densities are high, highlighting the importance of local site characteristics on populations, and suggesting relatively weak interactions between Ae. aegypti and Ae. albopictus. They also indicate local areas within hamlets where consistently high mosquito densities may influence Wolbachia invasions and other interventions.