Microalgae are considered promising biodiesel feedstock, however the genetic diversity and genomic evolution of microalgal traits underlying robust oil production remain ill defined.Here we presented a seven-member PhyloGenome of Nannochloropsis, a phylogenetic distinct group of wild unicellular microalgae capable of rapid growth and robust neutral-lipid production in large-scale cultivation.This unprecedented dataset systematically reveal the nature and degree of genomic conservation and divergence at the strain-, species-and genus-levels in microalgae.