When you go looking for airfares online, are you really getting the best deal possible?

Fareportal, an online travel agency behind flight booking websites like CheapOair and OneTravel, filed a lawsuit against budget airline JetBlue this week, accusing it of engaging in an anti-competitive "scheme" to prevent consumers from being able to comparison shop JetBlue’s airfares with other airlines.

The lawsuit alleges that JetBlue is making it hard for travelers to compare prices on routes it "dominates," allowing it to raise fares. Fareportal said JetBlue has blocked CheapOair and a dozen other online travel agencies from displaying its content.

Fareportal, an online travel agency behind flight booking websites like CheapOair and OneTravel, filed a lawsuit against budget airline JetBlue this week. (iStock)

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That could lead to higher ticket prices in markets where JetBlue has a strong presence like New York, Fort Lauderdale, Orlando, Boston, Los Angeles and San Juan, Puerto Rico, Fareportal claimed.

"JetBlue is trying to force customers to book tickets on its website where the lack of price comparison with fares from other airlines will allow JetBlue to raise ticket prices for price-sensitive travelers," Frederick Stein, Fareportal’s chief legal and compliance officer said in a written statement.

However, the airline disputed Fareportal’s allegations, calling them "frivolous and wholly without merit."

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"It is common industry practice for airlines to choose where to sell their products," a JetBlue spokesperson said via email. "We are currently one of several major airlines not selling via Fareportal’s platforms."

There are currently more than 10 aggregator and online travel agency sites that do include JetBlue fares in their comparison listings with other airlines, according to the JetBlue spokesperson. They also noted that its lowest fares will always be on its own website.

There are currently more than 10 aggregator and online travel agency sites that do include JetBlue fares in their comparison listings with other airlines. (AP)

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Fareportal said it serves customers in 195 countries and collaborates with more than 600 airlines. It filed the lawsuit against JetBlue in U.S. District Court for the Eastern District of New York Tuesday.

The lawsuit comes as JetBlue is holding its winter sale offering one-way tickets for as low as $49. The sale, for flights between Jan. 16 and June 17, runs through Jan. 12.