Despite the diversity and importance of Mollusca, evolutionary relationships among the eight major lineages have been a longstanding unanswered question in Malacology. Early molecular studies of deep molluscan phylogeny, largely based on nuclear ribosomal gene data, as well as morphological cladistic analyses largely failed to provide robust hypotheses of relationships among major lineages. However, three recent molecular phylogenetic studies employing different markers and more data have significantly advanced understanding of molluscan phylogeny by providing well-supported topologies and generally congruent results. Here, evolutionary relationships among the major lineages of Mollusca and implications of recent findings for understanding molluscan evolution are reviewed. Most notably, all three of the recent studies reviewed herein recovered a monophyletic Aculifera, a clade including Aplacophora (Neomeniomorpha Chaetodermomorpha; worm-like molluscs) and Polyplacophora (chitons). This finding argues against the previously widely-held notion of an aplacophoran-like ancestor of Mollusca. Also, these studies counter the widely held view that Gastropoda and Cephalopoda are sister taxa - a result with important implications for the field of neurobiology where representatives of both taxa are used as models. Surprisingly, the one study that sampled the limpet-like Monoplacophora recovered it sister to Cephalopoda. Placement of Scaphopoda remains ambiguous as two studies place it sister to a Bivalvia-Gastropoda clade (Pleistomollusca) with strong support but another places Scaphopoda sister to Gastropoda with strong support. Ongoing work in several labs employing new sequencing technologies and analytical methods as well as morphological and developmental studies will undoubtedly continue to improve understanding of deep molluscan phylogeny and evolution.