P.T. Punnoose married Rosamma Punnoos who was a Catholic and later leader of the Communist Party of India, in 1946. Punnoose was a Marthoma Syrian. No marriage between a Catholic woman and a Marthoma man had ever occurred in the region, at the time. Besides which, Rosamma's family supported the Indian National Congress, and objected to her marrying a communist. Furthermore, he was wanted by police and authorities who were conducting a crackdown against communists at the time. As with all Christian weddings between communist couples, at the time, the two were married at a church in Cochin with a specialletter of consent from the Pope. He had to be brought to the church quietly to evade to police. They have two children a daughter and son.