Disclosed is a transformation method whereby an ability to produce a useful substance of a stramenopile can be improved. The method for transforming a stramenopile comprises transferring a foreign gene into the stramenopile which is a microorganism belonging to the class Labyrinthula, more specifically, to a genus Labyrinthula, Altornia, Aplanochytrium, Schizochytrium, Aurantiochytrium, Thraustochytrium, Ulkenia, etc. Said foreign gene, which is a gene relating to tolerance against an antibiotic, a colorimetric protein and/or a fatty acid desaturase (Δ5 desaturase gene, Δ12 desaturase gene and/or ω3 desaturase gene), is transferred by using the electroporation or gene-gun technique.