Protists of the class Dinophyceae have long being recognized as important contributors to primary production in the world’s seas. With contributions ranging from carbon fixation to being responsible for various types of seafood poisoning, their impacts range from being important carbon fixers all the way to being a public health concern. Despite their ubiquity and importance, much has yet to be explored in terms of their genomic organization. A distinguishing feature of the group is the potential for extremely large genome sizes, which has so far prevented obtaining a complete genomic sequence. An alternative to genomic scale studies is to take a ‘snapshot’ of the transcriptome at a particular time and or environmental condition in order to gain insight into protein expression. 2nd generation sequencing technologies have made this possible on a large scale, however in the absence of a reference genome, de novo transcriptome assembly can be difficult and resource intensive. This study was designed as a direct comparison between transcriptomic assemblies generated for Polarella glacialis using two 2nd generation sequencing technologies, Roche 454 pyrosequencing and Illumina’s Solexa Sequencing-by-Synthesis. Libraries for both technologies were created from the same mRNA and assembled independently in house in order to test which technology and assembly algorithm yielded the best assembly. Annotation was then performed on the ‘best’ transcriptomic assembly obtained.