Ms May said there was “no place for violence” in politics and called for “tolerance, decent and respect”.
She said the intimidation was “unacceptable”.
Her comments come after a numbered Tory rebels received vicious abuse after they supported an amendment to the EU Withdrawal Bill.
Anna Soubry revealed she was sent messages saying she should be hung in public”.
Ms Soubry told the Guardian she had been attacked on social media and her office had received threatening messages.
She said: “I got an email from somebody yesterday saying: ‘In the past, traitors were taken out and shot’. It’s appalling”
Dominic Grieve, the ringleader of the revolt that saw Mrs May suffer her firs commons defeat, said he had received death threats.
The defeat saw 11 Tory MPs join Labour and the Liberal Democrats on Wednesday in backing an amendment that guarantees Parliament a “meaningful vote” on Brexit.
Another Brexit rebel, Sarah Wollaston, said she had also been targeted by online trolls.
Corbynista activists targeted the pregnant wife of an unnamed Tory MP after he challenged Labour leader Jeremy Corbyn in the Commons.
One vile Facebook user told her “I hope your baby dies”.
A report by the Committee on Standards in Public Life found social media was “the most significant factor” in driving harassment and intimidation of 2017 General Election candidates.
The report recommended: “Some have felt the need to disengage entirely from social media because of the abuse they face, and it has put off others who may wish to stand for public office. In the fast-paced and rapidly developing world of social media, the companies themselves and government must both proactively address the issue of intimidation online.
“Not enough has been done. The Committee is deeply concerned about the limited engagement of the social media companies in tackling these issues.”
The bitter atmosphere even prompted Archbishop of Canterbury, Justin Welby to step in and call for a Christmas truce.
Speaking to BBC, he said: “If we go back 103 years, we find Christmas 1914 there was a ceasefire. It would be very good to have a ceasefire from insult and the use of pejorative terms about people at this time”