Acidophilic microalgae play a vital role in primary production in acidic geothermal sites. As one of the important material of biofuel, their commercial values are increasing day by day. However, there is limited research on their species composition and community assembly which could be useful in microalgae culturing. Through using more comprehensive environmental measurements (e.g., temperature, pH value, concentration of ions, and chemical composition of soils) and NGS techniques, (using both 454 and Illumina platforms on 140 samples collected from 27 acidic geothermal sites across the West Pacific Island Chains.), we could have better understanding in their biodiversity and community assemblies. By integrating the community complexity and environmental parameters, we aim to better understand the relative roles of neutral and deterministic processes underlying their species diversity and community assemblies.  Having this basic knowledge about acidophilic microalgae, we could optimize our culture condition to improve their growth rate, quality, and oil content to gain more interest from these microbes.