Haptophytes are a key phylum of marine protists, including ~300 described morphospecies and 80 morphogenera. We used 454-pyrosequencing on large subunit ribosomal DNA (LSU rDNA) fragments to assess the diversity from size fractioned plankton samples collected in the Bay of Naples. One group-specific primer set targeting an overlapping region of the LSU rDNA D1/D2 region was used to amplify Haptophyte sequences from nucleic acid extracts (total DNA or RNA) of two size fractions (0.8-3 or 3-20 µm) and two sampling depths (subsurface, at 1m, or deep-chlorophyll-maximum (DCM) at 23m).