An ω-3 fatty acid desaturase gene which is involved in de novo synthesis of -linolenate was isolated from cDNA library of Perilla frutescens. A cDNA library was constructed with mRNA extracted from perilla seeds of 12 DAF. The cDNA clone consisting of 1317-bp open reading frame encoding 438 amino acids with a relative MW of 50 kDa, was isolated and showed 65-83% similarilties to other known genes. This cDNA is deduced to encode a plastidal ω-3 fatty acid desaturase based on the facet that it has higher homology to plastidal ones than to microsomal ones and its N-terminal sequence shares several characteristics of transit peptides of chloroplast proteins. Southern blot analysis of genomic DNA indicated that more than one gene or alleles for ω-3 fatty acid desaturase are present in the genome of perilla. Northern blot analysis showed that the ω-3 fatty acid desaturase gene is mainly revealed in early developing seeds and has different expression patterns depending on tissue types compared to the microsomal ones.