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Haematococcus pluvialis has attracted attention due to its ability to produce astaxanthin, which has many functions such as antioxidation and anticancer. In order to further understand its nitrogen metabolism, the transcription levels and the enzyme levels of glutamine synthetase (GS), glutamate synthase (GOGAT), and glutamate dehydrogenase (GDH) in the process of nitrogen assimilation were studied under different nitrogen concentrations after cloning their cDNA sequences. The cloned cDNA sequence of gs is 1438 bp, including a 178-bp 5′ untranslatable region (UTR), a 114-bp 3′ UTR, and a 1146-bp open reading frame (ORF), which encodes a protein of 381 amino acids. The gogat had a total cDNA of 4931 bp, including a 17-bp 5′ UTR and a 4914-bp ORF, which encodes a protein of 1637 amino acids. The gdh had a total cDNA of 1529 bp, including 131-bp 3′ UTR and a 1398-bp ORF, which encodes a protein of 465 amino acids. During cultivation the transcription levels of the three genes fluctuated slightly during the first 4 days and then declined significantly. At the fourth day, the highest level of the transcription of the three genes was at the nitrogen concentration of 1000 mg L−1. The enzyme level also fluctuated with culture time, which is positively correlated with the transcription level. This study may lay foundation for optimization of nitrogen concentration for cultivation of H. pluvialis.