Forum Moderators: Robert Charlton & goodroi
And second, be sure you use the dropdown to compare the same kind of search (All Searches, Web search, Image Search, Mobile and Directory)
Why the two would be extremely different may be lost in the back end code for Webmaster Tools - which has been known to give buggy data. I am not even sure where GWT gets traffic data - probably click tracking on the SERPs. But the data from Google Analytics comes from tracking done on your server and is the more dependable of the two sources