The primary difference between Snopes.com and FactCheck.org is that FactCheck.org focuses primarily on political issues, while Snopes.com investigates a wide variety of legends, rumors and other statements. Snopes.com also deals with politics, but it is not its main focus.
As of 2015, Snopes.com is a more informal site run by Barbara and David Mikkelson. The Mikkelsons became involved with debunking rumors through their interest in folklore. Snopes.com was originally a hobby, although its accurate debunkings gained enough popularity that the pair now works on it full time. Snopes.com covers chain emails, urban legends, current events and holiday legends. They often debunk popular stories spread on social media sites.
FactCheck.org is a more professional site affiliated with the Annenberg Public Policy Center. It focuses primarily on statements made by actual politicians during debates, campaign speeches and other events. These statements are sometimes inaccurate or misleading, and FactCheck.org works to debunk them. It does sometimes branch out into other current events, such as fears about disease epidemics.
Both sites are trustworthy bipartisan sources with no political bias. Both have occasionally been subject to accusations of bias, but independent checks of these sources have found no evidence of it. In 2009, an email circulated accusing Snopes.com of bias and making other false claims, but FactCheck.org investigated and found it to be untrue.