Under the deal, Microsoft said it will receive royalties from any Samsung device running Google Android, which means it will profit from the success of the mobile operating system, which is rapidly increasing in popularity.
"Through the cross-licensing of our respective patent portfolios, Samsung and Microsoft can continue to bring the latest innovations to the mobile industry," said Dr. Won-Pyo Hong, executive vice president of global product strategy at Samsung's mobile communication division.
The pair also pledged to co-operate in the development and marketing of the Windows Phone platform.
"Microsoft and Samsung see the opportunity for dramatic growth in Windows Phone and we're investing to make that a reality," said Andy Lees, president, Windows Phone Division, Microsoft.
"Microsoft believes in a model where all our partners can grow and profit based on our platform."
The deal with Samsung is the latest in a string of patent licensing agreements Microsoft has signed recently. Previous deals include Acer and Velocity Micro. The tech giant also signed a deal with HTC last year, which means Motorola Mobility is "the only major Android smartphone manufacturer in the US without a licence", Microsoft highlighted in a blog. Microsoft has already accused Motorola Mobility of infringing its patents.
Some industry commentators are speculating Samsung has entered into the deal to help its fight against Apple, which has claimed Samsung's Galaxy Tab 10.1 tablet PC infringes patents relating to the iPhone and iPad.