Molecular ecology is defined as a science that studies interactions between life system and environmental system, as well as the corresponding molecular mechanisms. By combining macro and micro aspects, molecular ecology could reflect the nature of ecological phenomena. The green microalga Botryococcus braunii is well known for its ability to accumulate large amounts of hydrocarbon, and it is attractive as a potential resource for renewable biofuel production. This review, on the base of briefly introducing the physio-ecological characteristics of B. braunii concerning morphology and chemical race, mainly addresses the up-to-date achievements of molecular ecology including molecular phylogeny and its relationship with chemical race, genome size and original geographical position. Morphologically, B. braunii is characterised by a botryoid organization of individual pyriform-shaped cells, held together by a refringent matrix containing lipids. In classical taxonomy mainly referring to morphology structures, it is difficult to identify whether B. braunii is a member of Chlorophyta or Xanthophyta, Recently, the molecular phylogenetic results based on 18S rRNA analysis clarified that this alga belongs to Trebouxiophyceae (Chlorophyta). According to the differences of the produced hydrocarbon, at least three chemical races of B. braunii could be identified, respectively named as Race A, B and L. Race A produces essentially odd-numbered n-alkadiene and triene hydrocarbons from C₂₃ to C₃₃; race B produces triterpenoid hydrocarbons (C_nH_2n-10, n=30-37), including C₃₀-C₃₇ botryococcenes and C₃₁-C₃₄ methylated squalenes; by contrast, the hydrocarbon product of the race L involves one single C₄₀ tetraterpenoid hydrocarbon, lycopadiene. In addition, the molecular phylogenetic analyses of B. braunii based on 18S rRNA gene sequences shows high consistency between the established phylogeny and the chemical races; meanwhile, there seems to be some correspondence between the alga evolutionary relationship and the hydrocarbon products. On the genomic level, the genome size is similar in race B (166.2Mb) and race A (166.0Mb) which are in far evolutionary relationships, whereas it exists significant differences between race B and race L (211.3Mb) which are from the same cluster. The significance of this discrepancy in terms of how these chemical races diverged is not clear at this time. Moreover, genetic relationship of this alga strain originally isolated from different geographical locations is established by molecular phylogenetic analysis, indicating both high genetic diversity in alga strains and high genetic polymorphism in DNA segments. To conclude, this review discusses some deficiency in the present research and suggests several critical issues that need further study. For instance, the genome and proteome of B. braunii to reconstruct main metabolic pathways which are responsible for lipid production should be sequenced. These finding will definitely aid in directly clarifying the molecular mechanisms of ecological phenomena, thus benefit both the theory development in molecular ecology and the practice process for alga-oil production.