Since the discovery of Phaeodactylum tricornutum by Bohlin in 1897, its classification within the tree of life has been controversial. It was in 1958 when Lewin, using oval and fusiform morphotypes, described multiple characteristic features of this species that resemble diatoms structure, the debate to whether classify P. tricornutum as a member of Bacillariophyceae was ended. To this point three morphotypes (oval, fusiform and triradiate) of Phaeodactylum tricornutum have been observed. Over the course of approximately 100 years, from 1908 till 2000, 10 strains of Phaeodactylum tricornutum (referred to asecotypes) have been collected and stored axenically as cryopreserved stocks at various stock centers. Various cellular and molecular tools have been established to dissect and understand the physiology and evolution of P. tricornutum, and/or diatoms in general. It is because of decades of research and efforts by many laboratories that now P. tricornutum is considered to be a model diatom species. My thesis majorly focuses in understanding the genetic and epigenetic makeup of P. tricornutum genome to decipher the underlying morphological and physiological diversity within different ecotype populations. To do so, I established the epigenetic landscape within P. tricornutum genome using various histone post-translational modification marks (chapter 1 and chapter 2) and also compared the natural variation in the distribution of some key histone PTMs between two ecotype populations (chapter 4). We also generated a genome-wide genetic diversity map across 10 ecotypes of P. tricornutum revealing the presence of a species-complex within the genus Phaeodactylum as aconsequence of ancient hybridization (Chapter 3). Based on the evidences from many previous reports and similar observations within P. tricornutum, we propose natural hybridization as a strong and potential foundation for explaining unprecedented species diversity within the diatom clade. Moreover, we updated the functional and structural annotations of P. tricornutum genome (Phatr3, chapter 2) and developed a user-friendly software algorithm to fetch CRISPR/Cas9 targets, which is a basis to perform knockout studies using CRISPR/Cas9 genome editing protocol, in 13 phytoplankton genomes including P. tricornutum (chapter 5). To accomplish all this, I used various state-of-the-art technologies like Mass-Spectrometry, ChIPsequencing, Whole genome sequencing, RNA sequencing, CRISPR genome editing protocols and several computational softwares/pipelines. In brief, the thesis work provides a comprehensive platform for future epigenetic, genetic and functional molecular studies in diatoms using Phaeodactylum tricornutum as a model. The work is an addon value to the current state of diatom research by answering questions that have never been asked before and opens a completely new horizon and demand of epigenetics research that underlie the ecological success of diatoms in modern-day ocean.