Molluscs comprise one of the most species rich animal phyla and exhibit incredible diversity in anatomy, development, ecology, and life history. Despite the extensive fossil record of Mollusca, phylogenetic reconstruction within the phylum has been controversial because some of the classes are highly modified. For the same reason, it has been difficult to identify the sister group to molluscs. With the advent of molecular techniques, a new array of characters has become available. Initially, nuclear ribosomal small subunit (18S) data was widely used and found to be useful in placing Mollusca within the bilaterian alliance known as Lophotrochozoa. These data have thus far proven to be of little use, however, in identifying the likely sister group within Lophotrochozoa to Mollusca or the relationships among the molluscan classes. A few other genes, notably complete nuclear ribosomal large subunit (28S), may have potential in resolving these questions. In addition to the sequence data, developmental genes and mitochondrial gene order data have become available for several groups and show great promise for future phylogenetic studies of Mollusca. Here we 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.