The Straits of Johor, a narrow strait that separates Southern Peninsular Malaysia from the island nation of Singapore, is an important marine aquaculture site that meets the demand for seafood from both countries. Urbanization, intensive anthropogenic activities, and shipping industries, however, have led to the deterioration of the coastal ecosystem health, with increasing events of hypoxia and harmful algal blooms (HAB). A hypoxic-anoxic dead zone, with dissolved oxygen levels ranging from 0.19 to 1.7 mg/L, was identified at the inner Johor Strait, covering an estimated area of 10.3 km². Prolonged high biomass diatom blooms that were triggered by eutrophication were identified as the cause of the formation of hypoxic-anoxic zones. In this study, the effect of hypoxia-anoxia on microphytoplankton communities was investigated by comparing the communities at the inner and outer parts of the strait. Microphytoplankton composition and the in situ water parameters of temperatures, salinity, pH, dissolved oxygen levels, macronutrients, and chlorophyll-a concentrations were collected at monthly intervals from May 2018 to April 2019. Our results showed that high biomass blooms (<50 μg/L chlorophyll-a) were dominated by diatom genera Skeletonema, Chaetoceros, Rhizosolenia, Thalassiosira, and the dinophytes Blixaea quinquecornis and Scrippsiella. In the inner strait, where nutrient concentrations were higher, a homogeneous bloom of high biomass microphytoplankton was observed with low species diversity compared to the outer strait. The outer strait displayed a diverse community of microphytoplankton assemblages, with a range of H' values from 1.91 to 3.15 and gradually decreased towards the inner part of the strait. The marine-influenced outer strait is more open and intermediate nutrient levels exhibited a stable pattern of heterogenous and higher diversity of microphytoplankton than in the more eutrophic conditions at the inner Johor strait.