Microphytobenthos (MPB) or benthic microalgae are recognized as the dominant flora in shallow neritic ecosystems such as mangroves. The diversity, biomass and community composition of microphytobenthos in selected mangrove ecosystems along the southwest coast of India were assessed. A total of 110 species of microphytobenthos classified under 49 genera were identified during the study. Nine subclasses of MPB were identified—subclass Bacillariophycidae, Fragilariophycidae, Urneidophycidae, Coscinodiscophycidae, Melosirophycidae, Thalassiosirophycidae, Biddulphiophycidae, Oscillatoriophycidae and Nostocophycidae. Division Heterokontophyta (diatoms) was the best-represented division followed by division Cyanophyta. Diatoms comprised 81% of the microphytobenthic community in the selected mangrove ecosystems, and among these, the pennate diatoms (93%) dominated the total diatom population. The major diatom genera observed during the study were Amphora, Navicula, Pleurosigma, Gyrosigma, Mastoglia, Diploneis, Cocconeis, Lyrella, Entomoneis, Caloneis, Bacillaria and Nitzschia. Episammic and epipelic diatoms were observed (Cocconeis sp., Pleurosigma sp.) along Kollam and Kannur, whereas at Kochi, epipelic diatoms were dominant (Nitzschia sp., Navicula sp.). The study also provides a spatial comparison between the microphytobenthic communities within the study area and can act as a baseline data for the trophodynamic studies of the highly diverse ecologically and economically significant mangrove ecosystems.