Iris halophila Pall and its variety I. halophila var. sogdiana (Bung) Grubov are potential horticultural plants for arid and saline-alkali land because of their drought and salt tolerant characteristics and various flower color. In order to elucidate the mechanism of different pigmentation in these two species, we cloned 3 partial segments of key genes relating to anthocyanin biosynthesis, namely chalcone synthase (CHS), chalcone isomerase (CHI) and flavonoid- 3',5'- hydroxylase like(F3'5'H-like), from perianth of young flowers of these two Iris plants. retro-transcription PCR method were employed in cloning and gene-specific primers were designed based on a transcriptome sequencing. The expression of these 3 genes were characterized by a real-time PCR assay. Sequence analysis showed that these 3 genes are first reported in I. halophila. Among these genes, F3'5'H-like is different from the classical F3'5'H which belong to CYP75A subfamily of cytochrome P450 superfamily, it is a homolog of Vanda coerulea F3'5'H-like gene which belongs to a new subfamily CYP76AB, a novel type of blue flower related genes. Expression analysis indicated that compared with in the yellow flowered I. halophila, CHS and F3'5'H-like are up-regulated in I. halophila var. sogdiana and are responsible for its blue-violet flowers.