Flores sustained the injury during training on Thursday and an MRI scan has confirmed Central Coast's worst fears.
The 2011 Johnny Warren medallist, who tops the Mariners' scoring charts with three goals, will require a knee reconstruction.
"It is my desire to improve every day, and for two hours each day I fight in training to be better," he said.
"Yesterday was the day that, unfortunately, the injury had to happen to me. I will remain strong and hope to come back one day to Bluetongue (Stadium) better.
"I trust in the medical team and trust that the Mariners as a family will look after me. Today I am in a little bit of pain, but I feel the support from everyone and I thank the fans for their support because they have been very kind to me.
"My wish for the team is to keep focused. We are in the fight to keep the (championship) trophy on the (Central) Coast and I believe in my team-mates."
The news is a major blow to Central Coast's hopes of defending their A-League crown with the club already set to lose New Zealand international Michael McGlinchey to J-League outfit Vegalta Sendai on a season-long loan following Sunday's clash with the Melbourne Heart.
"It is a bitter blow for Marcos and for the club," said coach Phil Moss.
"Over the coming months we will do whatever we can to help Marcos in his recovery and return to the game.
"Despite the loss of Marcos for this season we will continue to show that we are made of tough stuff here at the Mariners. We have the quality and the mental strength to continue moving in the right direction.
"We're fully focused on our first goal of making the Hyundai A-League 2013-14 finals series."
Flores is the sixth player to suffer a season-ending injury in 2013-14 after Mariners team-mate Adam Kwasnik (knee), Rhyan Grant (knee), Scott Neville (knee), Paul Ifill (Achilles) and Scott Jamieson (Achilles) had their campaigns cut short too.
