The deal to buy Barcelona-based Fogg is the Edinburgh company's largest yet and will see it bringing hotel search functions in-house for the first time.
Previously that was done through a partnership with Hotels Combined.
Skyscanner chief executive Gareth Williams promised users an extended and enhanced hotel search service in the coming months.
He said: "Our users are going to love hotel search as a result of this acquisition."
The Fogg business, which is being bought for an undisclosed sum, will also serve as a new Barcelona office for Skyscanner. The company expects to integrate the new system, currently available in English and Spanish, into its site and smartphone applications by the end of the year.
It also intends to improve the existing hotel search functions as well as extending them into the 30 languages it already caters for in other travel areas such as flights and car hire.
All five of Fogg's staff are transferring over with further hires in Spain likely as a result of the deal.
Mr Williams, who set up Skyscanner with friends Bonamy Grimes and Barry Smith in 2003, said the Fogg team shares the same passion for travel experiences as the company he runs. He added: "It makes them the perfect fit for us. We built the best flight search product anywhere in the world. We then expanded that offering into car rental.
"And we've taken a big step towards completing the picture in the space of hotel search."
Fogg uses semantic terms and also incorporates things such as average ratings, room information and rates from different existing search engines.
Carlos González, chief executive of Fogg, said: "After four years of building the fastest, most human hotel search engine, we're finally able to accelerate our ambitions by joining the world's fastest-growing international travel search company."
Skyscanner broke from its flight only strategy in 2009 by rolling out hotel and car hire services. It has since built a car rental search engine which runs in 200 markets around the world and the acquisition of Fogg is being seen as a fast-tracking of a similar process for hotels.
Skyscanner has already signalled it is gearing up for growth by announcing plans to double staff numbers from 250 to 500 in the coming years including 150 in Scotland. As well as its headquarters in Edinburgh, Skyscanner has bases in Glasgow, Singapore, Beijing and Miami.
Scottish Equity Partners remains the sole external investor in Skyscanner having paid £2.5 million for a stake in 2008.