The phylum Mollusca is one of the largest animal phyla with diverse body plans and an extensive fossil record. Some of the molluscan classes are so modified that phylogenetic reconstruction within the phylum, based on morphological characters has been controversial. With the advent of molecular techniques, sequence data has become an alternative source of phylogenetic characters. Initially, nuclear ribosomal small subunit (18S) data was widely used, mainly to understand the relationship of molluscs with other protostome groups. Recently, 18S data have been used to investigate relationships between the different classes. A few other gene fragments have been used to address relationships within certain classes. In addition to the sequence data, developmental genes and mitochondrial gene order data have become available for several groups. I intend to provide an overview of the current status for the different types of molecular data and what direction research is taking in the study of molluscan evolution with examples from the Bivalvia.