The unicellular green alga, Chlamydomonas reinhardtii is a model organism for studying various biological processes, such as photosynthesis, flagellar motility, and lipid metabolism. To find some novel genes regulating the lipid metabolism under various stress conditions, the paromomycin resistance gene aphVIII was transferred into the genome of C. reinhardtii to establish a mutant library. Two genes mutated in two of the TAG-reduced mutants (Cre06.g278111 in M2 mutant, Cre06.g278110 in M6 mutants) were neighboring in the genome, and their expression levels were down-regulated in their corresponding mutants in parallel with their reduced TAG levels following N deprivation. The proteins encoded by these two genes (KCN11 by Cre06.g278111, ACYC3 by Cre06.g278110) contained a conversed cyclic mononucleotide phosphate (cNMP) binding protein and an adenylate domain, respectively. Since cNMP binding protein and adenylate domain have been known as important components of cyclic adenosine monophosphate (cAMP) signaling pathway, suggesting that these two genes might affect cellular TAG biosynthesis through cAMP signal pathway.