Other than both coming from Apple and both running OS X Mavericks and both having an aluminum case, the differences are substantial. Karen Haslam does a good job comparing specifications:
Before Apple launched the new MacBook Pro with Retina display range we would have whole-heartedly recommended the MacBook Air. However, the addition of the lower priced entry-level Retina MacBook Pro means that the Pro laptops are now a much more attractive option.
Entry level 11-inch MacBook Air starts at $999 while the low end 13-inch MacBook Pro with Retina display is $1,299. The maxed out Pro gets to $3,299 very fast.