The tropical Red Sea coast of Saudi Arabia is dominated by intertidal soft sediments, seagrass meadows and mangrove beaches. These habitats have been under high pressure for decades partly due to anthropogenic activity. The water of the Red Sea is characterised by its high temperature and salinity throughout the year. The microalgae is a group of organisms characterised by their small size, unicellular or colonial organisation and ability or secondarily lost ability to photosynthesise including closely related non-photosynthetic species. The photoautotrophic microalgae are responsible for approximately 45% of the World's primary production and thus play a major role in many ecosystems. It is estimated that more than 40,000 algal species (including macroalgae) have been described, but recent advances in high throughput sequencing suggest there is a vast unknown diversity yet to be discovered. Little is known about the microalgal species diversity associated with the tropical habitats of the west coast of Saudi Arabia. Eleven strains were isolated in the shallow waters and beaches of Saudi Arabia. They were studied morphologically with light microscopy, scanning electron microscopy and transmission electron microscopy and molecularly with phylogenetic trees inferred from 18S and partial 28S (D1/D2) rDNA. Sixteen unique sequences and two previously recorded sequences were acquired and will be uploaded to NCBI GenBank. Four strains have been identified to species: Cafeteria roenbergensis Fenchel & Patterson, Lotharella reticulosa Ota, Cylindrotheca cf. closterium (Ehrenberg) Reimann & Lewin and Oxyrrhis marina Dujardin. The latter two have previously been recorded in the Red Sea. The first two have been recorded in similar habitats. Four strains have been identified to genus: genera Amphidinium Claparède & Lachmann, Chlamydomonas Ehrenberg, Nitzschia Hassall and Tetraselmis Stein, all of which are previously recorded in the Red Sea and similar habitats. Three potentially novel species with affinity for known species were partially described. They belong to genera Proteomonas Hill & Wetherbee, Pavlova Butcher and Rhizochromulina Hibberd & Chrétiennot-Dinet respectively.