The Indonesian island of Java, with a surface area of 126,566 km2 and a population of 115 million people, is one of the most densely populated regions on Earth. In the Menoreh Hills of Central Java, malaria cases increased between 1997 and 2001. From 2001 to 2003, the Indonesian Ministry of Health and U.S. Naval Medical Research Unit 2 (NAMRU–2) conducted a longitudinal study, examining Anopheles adult and larval bionomics in order to identify vector species in the region. Data from 5 ecologically independent study sites showed distinct seasonal patterns of adult mosquito activity and abundance of Anopheles species. The two main vectors incriminated were Anopheles balabacensis and An. maculatus. Another very common vector, but one which is usually considered to be minor, was Anopheles vagus, which was found to be sporozoite positive in 3 of the 5 villages surveyed. In the Sukabumi District of West Java, the rate of Plasmodium falciparum and P. vivax malaria has increased since 1998. The Indonesian Ministry of Health and NAMRU-2 are currently conducting a 12-month large-scale ecological study of the spatial distribution of Anopheles species in this region. To date, the study has identified and ecologically characterized over 1000 sites and identified 23 species of Anopheles. Anopheles barbirostris, a highly zoophilic species, is the most often collected. In addition, An. aconitus, An. maculatus and An. sundiacus have also been found. These species have historically played a major role in malaria transmission in West Java. In contrast to Central Java, no An. balabacensis have been collected in Sukabumi. Similarities and differences in Anopheles larval ecology between Central and West Java will be discussed along with its effect on disease transmission and impact on mosquito control operations.