The Austria international moves to the Potters for £2.6 million.
"Marko is a player we have been aware of for some time," says Hughes, "and I'm really pleased we have been able to add him to our squad. "He has played at the highest level in Holland, Italy and Germany and is keen to make his mark in England with Stoke City."
The cost of his transfer could increase by a further £850,000 if he proves a success during his four-year contract.
For the big stories and the banter follow us on Twitter: @tribalfootball