Haminoeidae is the most diverse family of Cephalaspidea with 13 to 17 genera commonly recognised as valid and with 46 genera that historically have been moved back and forth between Haminoeidae and other families. Due to poor definition of most genera the family is plagued by extensive taxonomic confusion and its generic composition and internal relationships remain uncertain. In this work we have integrated the study of type material, original descriptions, shells, morpho-anatomical data, and molecular phylogenetics (Bayesian, maximum likelihood, and maximum parsimony) based on five genetic markers (the mitochondrial genes cytochrome c oxidase subunit I and 16SrRNA and the nuclear genes 18SrRNA, 28SrRNA, and histoneH3) to delimit the valid genera, define synapomorphic traits, and establish synonym lists. Three hundred and ninety novel sequences were generated. In total 14 genera were recognised; one genus (Vellicolla gen. nov.) is here described as new and an additional fifteenth group was identified, but no species could be formally ascribed to it and therefore remains unnamed (here designated informally as mini-haminoeids). The relationships of genera are discussed and seven deep clades have been identified but are not formally named because of lack of recognisable synapomorphies for several of them. A new classification for Haminoeidae is proposed including 14 valid genera and one informal group.