The benzylisoquinoline alkaloids (BIA) are secondary metabolites that are produced by many of the Papaver species including Papaver bracteatum, Papaver pseudo-orientale, and Papaver orientale, three representative members of the section Oxytona Bernh. The sequences and expression levels of the genes positioned on the BIA biosynthesis pathway were previously defined in opium poppy (Papaver somniferum), one of the mostly studied species of the same genus. Nevertheless, the majority of predicted BIA-related gene sequences in the section Oxytona have not been specified. Here we are presenting new cDNA sequences that belong to the Oxytona species. In this study, partial sequences of norcoclaurine-6-O-methyltransferase (6OMT), NADPH-dependent codeinone reductase (COR), salutaridinol 7-O-acetyltransferase (SalAT), and (S)-tetrahydroprotoberberine cis-N-methyltransferase (TNMT) in P. pseudo-orientale; 3-hydroxy-N-methylcoclaurine 4´-O-methyltransferase (4OMT) in P. bracteatum; and TNMT and 6OMT in P. orientale were identified for the first time, and some of the previously sequenced genes were resequenced in the section Oxytona. Furthermore, expressions of those genes were also detected by using qRT-PCR in leaves. The findings were used to construct phylogenetic trees demonstrating the evolutionary relationships of BIA-related genes among Oxytona species.