Abstract: Objective Exploring the fatty acids contents regulation mechanism is needed. Method Two Δ-12 fatty acid desaturase gene sequences were got from Camellia oleifera developing seeds by transcriptome sequencing method, which named Cofad6 and Cofad2-2. The traits of the two genes and encoding proteins were compared, and the correlation of gene expression level and fatty acids contents were analyzed. Result Cofad6 has an open reading frame (ORF) of 1 347 bp and encodes a 448 amino acid (AA) protein; Cofad2-2 has an 1 152 bp ORF and encodes 383 AA protein. According to the alignment results, the CoFAD6 has the 65.7%83.68% amino acid sequence similarity with the FAD6 from other species, CoFAD2-2 amino acid sequence exhibits the highest similarity with C. chekiangoleosa (99.22%), and has the 78.59%~81.72% amino acid sequence similarity with FAD2 from other species. CoFAD6 and CoFAD2-2 have a fatty acid desaturase domain both, which means they belong to acyl-CoA desaturase family. CoFAD6 and CoFAD2-2 are transmembrane proteins and the CoFAD2-2 has a microbody C-terminal targeting signal motif. Real-time PCR analysis shows that Cofad6 and Cofad2-2 are both expressed in the developing seed of C. oleifera ‘Changlin No.4’. The expression level of Cofad2-2 is on the decline with the developing of seed, the variation trend is similar with that of linoleic acid content and opposite with that of oleic acid content. Conclusion It is indicated that Cofad2-2 gene might be one of the key genes to regulate oil quality in C. oleifera seed. This research provides scientific basis for oil quality improvement and molecular breeding in C. oleifera.