The colonial unicellular freshwater green alga Botryococcus braunii has recently attracted attention from the biofuel industry because of its unique traits to biosynthesize extraordinarily large amounts of hydrocarbon oils resembling petroleum constituents and to accumulate the oils within the colony. The purpose of this study was to evaluate B. braunii in terms of codon compatibility with other organisms in view of genetic engineering applications. Here, GC contents and codon usage were compared among three strains of B. braunii (BOT-88–2, BOT-22, and BOT-70), three other species of Chlorophyta (green algae), five species of the Streptophyta (land plants), and eight species of other phyla including bacteria, archaea, fungi, and mammals. Interestingly, B. braunii exhibited GC contents remarkably lower than the other Chlorophyta species and it also had an unbiased codon usage unlike other green microalgae. Codon usage of B. braunii rather resembled bacteria, animals, and land plants. Our results indicated that genes derived from various nonmicroalgal species could readily be expressed in B. braunii with relatively minor codon usage optimization, and vice versa.