FORTUNE — The past several years have been sluggish ones for the travel industry, and it’s unlikely to get better: Fiscal uncertainty in the U.S., a sovereign debt crisis in Europe, economic slowdown in China. In the online-travel industry, the sluggishness is separating the strong companies from the weak.

A look at the stock performance of several online-travel companies shows their fates diverging. On the happier side, Expedia’s (EXPE) stock is up 94% this year, while Priceline’s (PCLN) is up 31%. Among the less fortunate: Orbitz’s (OWW) stock is down 46% and Travelzoo’s (TZOO) is down 32%. Since the web began to make online bookings available in the mid-1990s, online travel has grown to account for a third of the global travel market. This year, global online travel bookings are expected to reach $313 billion, according to PhoCusWright, a travel-industry research firm.

For most of that time, sites like Priceline, Expedia and privately held Travelocity stole market share away from offline travel agencies as well as airlines and hotel chains. During and after the recession of the late 2000s, that trend has continued with travel sites like Priceline growing faster than travel-industry suppliers. But PhoCusWright sees that changing in the next couple of years as the travel industry pushes to reach travelers directly.

In numbers released Monday, PhoCusWright estimated that the U.S. online travel market will grow 11% in 2012, outpacing the 8% growth of the broader travel industry. Over the next two years, however, online-travel growth will is expected to slow to 7% a year, thanks to fiscal and economic uncertainty in the U.S. and slowdowns in Europe and Asia.

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Even worse for booking sites like Expedia and Priceline, most of that online growth is coming from online bookings made through airlines and hotels directly, a segment that is expected to grow 14%, versus 6% growth for online travel hubs. That slowdown is likely to hurt some online-travel sites more than others. Analysts are expecting Priceline’s revenue to increase by about 20% this year as well as 2013. Expedia’s revenue, meanwhile, is expected to increase by 15% a year. Orbitz, by contrast, is forecast to see revenue remain flat this year.

Smaller companies are also likely to see mixed fortunes. Analysts expect Kayak (KYAK) to see revenue growing between 25% and 30% this year and next, faster than the anticipated growth of its new parent, Priceline. TripAdvisor’s (TRIP) growth will be closer to 19%. TravelZoo will see about 6% growth, in line with the industry forecast.

Increasingly, however, the online-travel market is turning into a two-way race between Priceline and Expedia. Both are making bold moves, albeit dramatically different ones. Last December, Expedia spun off TripAdvisor and has been focusing spending on technology investments as well as a push into Europe, a longtime Priceline stronghold. Priceline recently paid $1.8 billion for Kayak, giving it a strong presence in the meta-search industry for travel.

Analysts aren’t expecting a wave of consolidation to follow the Kayak deal. More likely is the occasional acquisition that has happened in the space: Google buying ITA Software for $700 million and TripAdvisor buying Holiday Watchdog for an undisclosed sum.

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Future deals are likely to happen among companies active in the mobile space. Part of Kayak’s allure as an acquisition target comes from its appeal to smartphone owners. Kayak said queries on mobile devices doubled to 109 million in the first half of 2011, compared with a 30% increase in website queries to 505 million.

Mobile travel searches are currently seeing the same kind of growth that website searches saw a decade ago. And the market still has further to grow. In 2009, a quarter of business travelers used a mobile device to access travel information, according to eMarketer, a figure that will rise to 57% this year. Leisure travelers are following suit: Only 8% of them used mobile devices for travel information in 2009, versus 38% this year.

Online travel sites have room to grow even in a maturing market and a sluggish global economy. But no longer is the growth going to be across the board. Instead, it will concentrate among a handful of leaders like Expedia and Priceline, especially those that can make early inroads into new areas like the mobile web.