Abstract. Zakiyah U, Mulyanto, Suwanti LT, Koerniawan MD, Suyono EA, Budiman A, Siregar UJ. 2020. Diversity and distribution of microalgae in coastal areas of East Java, Indonesia. Biodiversitas 21: 1149-1159. Indonesia is well known as one of hotspot for biodiversity, including marine resources. However, Indonesia biodiversity has declined rapidly due to the changes in the aquatic environmental quality as the consequence of human activities. Biodiversity loss has been well studied in larger organisms, however, less is known for microorganisms, such as microalgae. Microalgae have received much attention recently due to its potential as renewable energy sources. This study aimed at describing biodiversity and distribution of microalgae in coastal areas of East Java and Madura, Indonesia. Six sites, i.e. Trenggalek and Sendangbiru representing south coast, Banyuwangi and Situbondo representing north coast of East Java, Pasongsongan and Pamekasan representing Madura north and south coast, respectively were sampled, which representing different background of anthropogenic development in these areas. Results showed that seawater condition in all sites is still good, with average pH 8.0 despite intense human activities, such as ecotourism, fishing and boat harbor, as well as residential area that has the potential to produce a lot of waste. Totally, there were 35 genera from all locations with varying abundance in each location and diversity index ranging from 1.105-3.312. Although most genera belonged to Bacyllariophyta, domination indices showed that there was not any single specific domination in all locations. Morisita indices showed that most distribution gave positive values indicating clumped dispersion of microalgae in all locations. Higher Shannon-Weaver indices characterized the south coast of East Java and Madura compared to the north coast of East Java area, which corresponded with lower dominancy indices.