Grant McCann's side earned promotion back to the Championship at the first time of asking and claimed the League One title after they finished two points ahead of second-placed Peterborough United.
Striker Wilks ended the season with 21 goals and nine assists across all competitions while Elder provided a goal and 10 assists from defence.
Honeymoon provided the most assists for Hull last season, helping to set up 13 goals while claiming four of his own. Coyle proved an important cog in City's promotion-winning machine, with the defender appearing 34 times in all competitions last season.
The rest of the League One side is made up by Posh striker Jonson Clarke-Harris, Sunderland’s Charlie Wyke and Aiden McGeady, Blackpool goalkeeper Chris Maxwell, Lincoln duo Lewis Montsma and Jorge Grant and Oxford midfielder Rob Atkinson.
Despite reaching the Championship play-offs, Barnsley did not have any players nominated for the Championship team of the year with Norwich City dominating the selections with six players.
The Canaries secured an emphatic and instant return to the Premier League, finishing six points clear at the top of the table with 97 points.
Goalkeeper Tim Krul, defenders Max Aarons and Grant Hanley, midfielder Emiliano Buendia, Tottenham loanee Oliver Skipp and striker Teemu Pukki were all voted into the divisional team by their peers.
Brentford's play-off success over Swansea City saw them earn three selections with 33-goal striker Ivan Toney, centre-half Ethan Pinnock and left-back Rico Henry all featuring.
Blackburn Rovers striker Adam Armstrong - who scored 26 goals in a team that finished the season in 15th - and Reading midfielder Michael Olise, were also named in the side.
Former Bradford City striker James Vaughan celebrated his retirement by being named in the League Two PFA team of the year.
Champions Cheltenham Town have Ben Tozer and William Boyle named in the XI, with Cambridge’s Kyle Knoyle, Wes Hoolahan and the prolific Paul Mullin also in.
Defender Ricardo Santos and striker Eoin Doyle represent promoted Bolton Wanderers while Salford goalkeeper Vaclav Hladky, Newport County's Josh Sheehan and Matt Jay of Exeter City make up the remainder of the side.
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