The invention provides marine microalgae delta6-fatty acid desaturase, and coding genes and application thereof. The delta6-fatty acid desaturase is provided with amino acid sequences shown in a sequence table SEQ ID NO.2 or amino acid sequences which are formed by replacement, shortage or addition of one amino acid residue or a plurality of amino acid residues and have the same functions. The delta6-fatty acid desaturase can effectively catalyze Linoleic Acid (LA, 18:2delta9, 12) to generate gamma- Linolenic Acid (GLA, 18:3delta6, 9, 12) and catalyze alpha-Linolenic Acid (ALA, 18:3delta9, 12, 15) to generate Stearidnoic Acid (SDA, 18:4delta6, 9, 12, 15).