Indonesia has rich Anopheline (Diptera: Culicidae) mosquito species living in various types of ecosystems. The study was conducted to profile and compare Anopheles diversity, equitability, and dominance in various ecosystems using different animal-based sampling techniques. The present study analyzed a subset of data collected from a nation-wide vector and animal reservoirs survey in 2016. Analyses were restricted to three ecosystem types (forest, nonforest, and coastal areas) in Java and Sumatera Islands. A total of 5,477 Anopheles were collected by using animal-baited (n = 1,909) and animal-baited trap nets (n = 1,978), consisting of 23 Anopheline species. Overall, Anopheles vagus was the most abundant species, followed by An. subpictus and An. barbirostris. Among the three ecosystems, the forest had a higher diversity index (H′ = 1.98), but each ecosystem has its specific predominant species. Compared with the animal-baited method, the Anopheles abundance collected by animal-baited trap nets was two-fold higher. Ecosystem, elevation, and sampling methods were associated with the abundance of female Anopheles (P-value < 0.001). Our findings revealed that Anopheles were found in a different ecosystem, indicating the potential of malaria transmission.This suggests that improved malaria vector surveillance is essential in all types of ecosystem. Furthermore, the study suggested that animal-baited trap nets could be used as the standard method of outdoor resting sampling in Indonesia in addition to the traditional human landing collection approach.