At the moment, Microsoft has two separate app stores, one for Windows and one for Windows Phone, although according to a recent report, this may be about to change.
According to The Verge, Microsoft plan to have one app store for Windows Phone and Windows devices, and this new App store will be available with the next release of Windows and Windows Phone.
The next release of Windows Phone is 8.1 and the next release of Windows is also 8.1, both of these new versions are due early next year, so we can expect to see the new unified Windows Store at the same time.
Source The Verge