Rising pace bowler Nathan Coulter-Nile was also a notable omission from the contracted list which is updated annually and was cut back from 20 to 18 players.
Doolan played in all three Tests on the recent tour of South Africa, scoring 186 runs at 31, while Marsh made successive ducks after scoring 148 in the first Test at Centurion and was dropped for the series decider.
Hughes was on the tour but did not play in the Test series.
"Alex Doolan was close to receiving a contract and he is highly regarded by the selection panel as the incumbent number three batsman in our Test line-up," chief selector John Inverarity said.
"He made his Australian debut less than two months ago and we look forward to him building strongly on the promising start he made in the three-Test series in South Africa.