Objectives To optimize the cultivation media for the growth rate of Haematococcus pluvialis and to study the transcription regulation of the algal nitrate reductase (NR), a key enzyme for nitrogen metabolism. Results The NR gene from H. pluvialis hd7 consists of 5636 nucleotides, including 14 introns. The cDNA ORF is 2718 bp, encoding a 905 aa protein with three conserved domains. The NR amino acids of H. pluvialis hd7 are hydrophilic and have similarity of 72% compared to that of Dunaliella. NR transcription increased with an increase of nitrate concentration from 0.4 to 1 g/l. A deficiency of nitrogen increased NR transcription significantly. The transcription level of NR increased at phosphorus concentrations from 0.08 to 0.2 g/l, with a maximum at 0.08 g/l. The optimum parameters of medium component for transcription of NR and growth of H. pluvialis were 0.3 g NaNO3/l, 0.045 g KH2PO4/l and 1.08 g sodium acetate/l. Conclusions This study provides a better understanding of nitrate regulation in H. pluvialis.