Malaria is a major health burden in the border-belt areas of Bangladesh. There are recent data from adult mosquito collections that a number of vectors are involved in the transmission cycle. However, little information regarding the larval habitats of Anopheles mosquitoes are available in Bangladesh. To start filling this gap, a cross-sectional larval survey was conducted in Bandarban, Bangladesh from October 2011 to September 2012. Descriptive analysis, Poisson regression, spearman correlations and zero-inflated Poisson regression were used to calculate the degree of association between the abundance of larval Anopheles species and environmental factors. From the 300 larval habitats sampled, 5,568 Anopheles larvae were collected and of these, 2,263 (40.6%) were identified to species. Collections represented 16 Anopheles species with Anopheles vagus (26.4%, n = 598) as the dominant species. A total of 16 Anopheles larval habitat types were identified. Larval abundance was significantly different (P < 0.05) among habitats with pond (40%, n = 914) and rice field (34%, n = 779) implicated to be the most utilized. Larval abundance varied significantly (P < 0.05) with habitat characteristics. Most of the larvae were collected from sites with a range of pH from 7.0 to 8.0. Data obtained from this study revealed both natural and human-created larval habitats were favorable for anopheline larval survival and development. Such information elucidates plausible drivers of high anopheline diversity, high vector abundance, changes in relative species abundance from historic data, and sustained transmission of malaria in endemic areas of Bangladesh.