A former MLA, Krishnankutty told reporters that he had faxed his resignation letter to SJD President M P Veerendrakumar.
Krishnankutty said he would retain his membership in the party and would concentrate more on the issues in the agriculture sector.
Reacting to Krishnankutty's decision, Veerendrakumar said if he had not resigned on his own he would have been removed from the party post since he had been working against the party line for quite some time.
The seat, which Krishnankutty won several times, was contested and won by a Congress candidate, the lead partner of the UDF.
He had also shared platform with some of the critics of SJD leadership.