A floristic survey of the marine algal biodiversity of Antsiranana Bay, northern Madagascar, was conducted during November 2018. This represents the first inventory encompassing the three major macroalgal classes (Phaeophyceae, Florideophyceae and Ulvophyceae) for the little-known Malagasy marine flora. Combining morphological and DNA-based approaches, we report from our collection a total of 110 species from northern Madagascar, including 30 species of Phaeophyceae, 50 Florideophyceae and 30 Ulvophyceae. Barcoding of the chloroplast-encoded rbcL gene was used for the three algal classes, in addition to tufA for the Ulvophyceae. This study significantly increases our knowledge of the Malagasy marine biodiversity while augmenting the rbcL and tufA algal reference libraries for DNA barcoding. These efforts resulted in a total of 72 new species records for Madagascar. Combining our own data with the literature, we also provide an updated catalogue of 442 taxa of marine benthic macroalgae from Madagascar, comprising 85 Phaeophyceae, 1 Compsopogonophyceae, 240 Florideophyceae and 116 Ulvophyceae. This diversity holds 29 (ca. 6.5%) endemic species to Madagascar. Our results are discussed in the context of increasing threats to biodiversity on Madagascar s coastal reefs from both anthropic and anthropogenic activities including sewage effluent runoffs and unsustainable agricultural practices such as massive deforestation, leading to ecosystem shifts to algal dominance on reefs, which are recommended to be addressed through integrated land-sea management in a Reef-to-Ridge conservation approach.