An updated checklist of Mozambican marine brachyuran crabs is generated based on an exhaustive revision of the existing literature, together with the additional records provided by the specimens collected throughout the three “MOZAMBIQUE” surveys carried out in Mozambican waters during three consecutive years (2007–2009) by the Instituto Español de Oceanografía, (Spanish Institute of Oceanography, IEO). A total of 269 species, grouped in 15 superfamilies, 26 families and 172 genera are reported in the checklist, and a detailed inventory is produced with the list and remarks about the brachyuran species collected. Thirty-nine crab species belonging to 19 families were identified based on morphological characteristics and/or genetic tools. DNA barcode sequences (16S rRNA and/or COI) were obtained for 37 species, including 16S and COI sequences that are new for 26 and 14 species, respectively. Colour photographs of fresh specimens illustrate the comments about most species, being the first time that the original colour pattern is described for some of them. New records in Mozambican waters are reported for the species Paromolopsis boasi, Mursia aspera, Carcinoplax ischurodous, Tanaoa pustulosus, Euclosiana exquisita, Oxypleurodon difficilis, Naxioides robillardi, Samadinia galathea, Cyrtomaia gaillardi, Paramaja gibba, Pleistacantha ori, Parathranites granosus, Parathranites orientalis, Ovalipes iridescens and Charybdis smithii, and second records for Moloha alcocki, Samadinia pulchra and Charybdis africana. In addition, Raninoides crosnieri, S. galathea and P. ori were collected for the first time after their descriptions. The female of Samadinia galathea is described for the first time, and a potential new species of Mursia is reported. Some records expand the known bathymetric range of certain species and/or their general distribution. New molecular and morphological data suggest the necessity of the revision of P. boasi, R. crosnieri, C. africana and the genera Platymaia and Carcinoplax. The variability and taxonomic validity of some morphological characters in brachyuran systematic is discussed.