Species in the microalgal genus Nannochloropsis are increasingly used as models for theoretical and applied studies. Here we attempt to generate InDel variations in the genome of Nannochloropsis oceanica, and then decipher the genetic basis of its economic and biological traits with bulked mutant analysis modified from bulked segregant analysis. In addition, we describe our efforts to construct site-tagged and gene-traceable mutant libraries to clone its genes through reverse genetic approaches. Currently, more than a half of N. oceanica protein-encoding genes are annotated against databanks. However, no functional gene has been de novo cloned from N. oceanica and no new function has been assigned to any of its annotatable genes. Here, we discuss the possible methods and potential benefits of de novo cloning of N. oceanica genes.