Pseudo-nitzschia multistriata is a toxic marine planktonic diatom that blooms regularly in the Mediterranean Sea. The species has a heterothallic mode of reproduction with two distinct mating types. This thesis aimed at exploring the molecular underpinnings of different stages of the sexual reproduction phase in Pseudo-nitzschia multistriata using genomics and transcriptomics approaches. A comparative transcriptomics approach was used to explore the molecular mechanisms involved in the early stages of sexual reproduction in which the opposite mating type strains engage in complex chemical communication and subsequent intracellular signaling. The present thesis identified a number of MT specific genes that are differentially regulated during sexual reproduction. The majority of these MT specific genes could not be annotated using homology based methods, suggesting that they have unique roles in this species. Further, substantial differences between the two mating types were observed in terms of metabolic processes employed during sex. Interestingly, a cell cycle arrest, a phenomenon extensively studied in yeasts, at the onset of the sexual phase was observed in Pseudonitzschia multistriata. Moreover, the genome of Pseudo-nitzschia multistriata along with other four diatom genomes was searched to look for the genes involved in meiosis. Although the majority of meiosis related genes could be identified, a few meiosis specific genes seem to be absent in diatoms, representing a case of lineage specific independent loss, observed in other sexually reproducing species. Lastly, genetic modification methods such as biolistic transformation and chemical mutagenesis were established for gene function studies in this species and the biolistic transformation is already being used to decipher the function of selected sex specific genes identified from RNA-seq experiments.