Diatoms are a highly productive and diverse class of unicellular marine eukaryotes, carrying out 25% of the world’s photosynthesis and generating ~ 40% of organic matter produced by the ocean each year. The diatom Leptocylindrus Cleve is a major component of phytoplankton blooms in coastal ecosystems and upwelling regions worldwide and although reported from Australia since the 1930s, there is little known about this genus in the southern hemisphere. Using light and transmission electron microscopy and molecular phylogenetics based on the nuclear-encoded ITS1/5.8S/ITS2 rDNA region, our study has characterised three species, L. aporus, L. convexus and L. danicus, from 55 clonal isolates. Using Illumina high throughput sequencing technology, de novo genome assemblies are currently being examined to characterise and compare the genome architecture of these three species. Furthermore, by mapping the genomes of multiple strains of L. danicus, our study aims to investigate the intraspecific diversity of diatom populations along this coastline. It is envisaged that both inter-species and intra-species genetic information on these ecologically significant diatoms will provide critical insights into modes of evolution, stress response and the adaptive capacity of marine organisms to changing ocean conditions.