An interspecific cross between P. citriodora and P. hirtella constitutes ideal material for a linkage map construction in genome project of Perilla. The chromosomes of the species are same with n=10 and progenies of the cross are normal in growth and seed set. The phenotype of F2 population of the cross are normally distributed and this is a proof of high affinity of the chromosomes during their sexual reproduction. Rosmarinic acid, Luteolin and Apigenin contents of F2 plants were distributed in similar range with tetraploid perilla cultivars. Luteolin and Apigenin are positively correlated with correlation coefficient of 0.762. 21 QTLs were detected in agronomic traits and Rosmarinic acid, Luteolin and Apigenin contents. Even though Luteolin and Apigenin are positively correlated, QTLs were located in different position. Purple leaf color related QTL was mapped in Chromosome 3 with LOD of 14.3, PVE of 50.4%. Three anthocyanin biosynthesis transcription factor like sequences, WD40 repeat-like superfamily protein, myb domain protein 43 and basic helix-loop-helix (bHLH) DNA-binding superfamily protein, were detected near from the QTL.