We were looking for self-catering accommodation and that is less well served in the town. We have stayed several times at Athanor House self-catering apartments and have been very happy there. Athanor House offers two flats for rent to visitors - a large luxury flat (though not at a luxury price) and a small studio flat. They come with a lovely garden complete with apple tree and views of the castle.
The house is central, close to the restaurants and attractions. It has a secluded garden where you can sit under an old apple tree and look over the town. Hannah, the owner of the house, lived for many years in London, speaks perfect English and is able to cater for our needs (including real English teabags!). An important consideration if you intend to use Cesky Krumlov as a base for touring Southern Bohemia is free car parking, some hotels and bed and breakfasts do not provide this.