The 29-year-old has struggled to recapture his place in the 43-year-old’s starting XI following an injury because of the emergence of George Hirst.
And a small minority of fans at Fratton Park voiced their dissatisfaction with the striker's appearance from the bench against the Shrimps last Saturday.
Marquis is a player who splits opinion among the Fratton faithful as he struggles to replicate his Doncaster Rovers form on the south coast.
He’s scored four goals in 20 appearances this season, while overall has 36 goals from 117 outings in his second spell at PO4.
But Cowley was quick to defend his forward’s attitude - despite not hearing the dismay from sections of the crowd.
Speaking to The News he said: ‘I didn’t hear it so I couldn’t comment.
‘John’s attitude has been very good, though. He’s a very good professional, he works incredibly hard.
‘We know what he can give the team, he’s had a period out of the team where the team has done well.
‘He’s working every day to try to create the opportunity to start again. When he’s not started but come on, he’s contributed to the group.’
Hirst has come of age in recent weeks and has spearheaded a newly-sharpened Pompey attack.
The 22-year-old netted his maiden EFL goal in the 3-0 victory over Lincoln and his tally of two doesn’t highlight his promising displays.
And Cowley outlined the benefits of having different types of strikers within his ranks.
He continued: ‘George and John are different and they have different attributes.
‘Within a squad it's good to have players with different attributes.
‘I would say John is more a number nine where I think George is a nine and a half - because you can play into and up to George.
‘You can also play down the sides to George and his movement ahead of the ball is very good and he’s carried some real goal threat for us.
‘John’s game is all about stretching the pitch with his movement and also he’s incredible at pressing.
‘John has the ability to be our first defender and play with a huge energy and intensity. So they’re slightly different profiles as players.’
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