Mr McGuinness, 66, died in hospital after suffering with a rare heart condition. He was the Northern Ireland deputy first minister and a former IRA commander.
Albion defender Shane Duffy took to Twitter, and said: “More tragic news this morning, RIP Martin Mc Guinness a true hero for many of us god bless your family and close ones #ireland.”
But he was criticised by some followers.
Allan McRitchie said: “God bless his victims and their families and loved ones, murderer and terrorist nothing more, and you play for Brighton.”
Another, Olly Dillingham simply said: “Grand Hotel BRIGHTON? Shameful!”
Oliver Allan said: “A truly ridiculous tweet considering who he plays for.”
But Mr Duffy responded: “I’ll always stand by what and who I support, it’s the way I was brought up.”
Five people were killed in the attack on Brighton’s Grand Hotel, which was holding the Conservative Party conference at the time.