Travel agents typically use something called a “global distribution system” (there are three or four major GDS and several smaller ones) but I think some online sites also rely on them so that's not the whole explanation for the lower price.
It's also possible that your travel agent is affiliated with a tour operator (TUI, Thomas Cook, etc.) and gets special rates through this channel. Tour operators typically buy hotel stays, seats on a regular flight, charter a plane, etc. and repackage everything in a all-inclusive tour but can also sell individual services. Since they buy in bulk several months in advance, they can negotiate better rates. For the hotel, it means less risk and less overhead compared to selling the rooms one-by-one, which is a good reason to offer these lower rates.
Also make sure to compare like with like, especially regarding things like cancellations, booking change, etc.