As a result of internal disagreements within the Wrexham Labour Party, he was deselected as the Labour Party's candidate in the Welsh Assembly elections of 1 May 2003, as a result of which he stood for the John Marek Independent Party and was successfully elected, defeating the official Labour Party candidate, Marek's former secretary, Lesley Griffiths. Were it not for the very low turnout in the Assembly election, Marek would certainly have lost his seat, as his re-election as a JMIP AM was more to do with his undoubted ability to mobilise his hard-core supporters, than any discontent with the Morgan executive(as the results across Wales showed there was very little), or as any reputation as a good AM.