To elucidate the mechanism underlying the enhanced growth rate in the Haematococcus pluvialis mutated with 60Co-gamma rays and domesticated with 15% CO2, transcriptome sequencing was conducted to clarify the carbon metabolic pathways of mutant cells. The CO2 fixation rate of mutant cells increased to 2.57 g L-1 d(-1) under 15% CO2 due to the enhanced photosynthesis, carbon fixation, glycolysis pathways. The upregulation of PetH, ATPF0A and PetJ related to photosynthetic electron transport, ATP synthase and NADPH generation promoted the photosynthesis. The upregulation of genes related to Calvin cycle and ppdK promoted carbon fixation in both C3 and C4 photosynthetic pathways. The reallocation of carbon was also enhanced under 15% CO2. The 19-, 14- and 3.5- fold upregulation of FBA, TPI and PK genes, respectively, remarkably promoted the glycolysis pathways. This accelerated the conversion of photosynthetic carbon to pyruvate, which was an essential precursor for astaxanthin and lipids biosynthesis. (C) 2017 Elsevier Ltd. All rights reserved.