"I got a threatening phone call few days back. The caller said that I and my family will be killed in three days. So, I have decided to leave Kashmir," Marcos told PTI.
He said he had passed the information to the local police but they have not been cooperative.
Marcos said it all started in Jan when one of his dogs was mysteriously killed a couple of days before the Republic Day celebrations.
"The next day my second dog was poisoned and a couple of days later, my vehicle was vandalised and the brakes failed," he said.
Marcos claimed that the authorised service dealer for his Mahindra vehicle told him that the ''brake failure'' was not accidental but a deliberate act of sabotage.
"I had come here to teach young people football but when my security and that of my family is compromised, I better leave this place," he added.
Marcos arrived in Kashmir four years ago on a short visit but decided to set up a permanent base after being impressed by the raw talent here.
He set up an academy and sent three players to Brazil for training with some leading clubs under an exchange programme which saw some upcoming players from the Brazil visiting Kashmir as well.
Sources in the Jammu and Kashmir Football Association said the threats and attacks on Marcos were handiwork of some disgruntled elements including a senior player from the valley and a local club affiliated with the Association.
"They have been carrying out a false propaganda against Marcos that he is preaching Christianity in Kashmir, which is a bundle of lies," an official of the JKFA said on condition of anonymity.
The official said the initiative of the Argentine coach had unnerved some vested interests as it has spread the game across the valley.
"Now the aspiring footballers did not need to lick to boots of a few club owners. There was an alternative and these vested interests want to wipe out that alternative," he added.
The official said all the programmes of Marcos in the valley were being run under the aegis of the JKFA.
The official said the Association was helpless and could not act against these elements as police has not acted on the complaint filed by the coach.
A senior police official said Marcos was living in a protected area and as such faced no threat. "We will find out what exactly the problem is. If he is worried about his security, we will ensure that he does not leave on that count," he added.
Marcos has been in trouble several times in the past as well. He was beaten up by security forces at the height of Amarnath Land Row agitation in 2008 but the matter was later resolved amicably.
He was asked to leave the country last year as the Union Home Ministry had refused to extend his stay in the valley.
Chief Minister Omar Abdullah intervened to ensure that he continues to coach the youth of the valley.