Currently, Chrome will open PDFs using whatever software you have set as the system default (usually Foxit or Adobe Reader). However, the browser's development build was recently tweaked to always open PDFs using Chrome's in-built reader, a change that's been made because "it's safer".
Image: Double-J Design / Licensed under Creative Commons 3.0. Image is modified.
According to Chrome "Happiness Evangelist" François Beaufort, this change is already in effect in the latest Canary builds of Chrome. There's no timeline however as to when we'll see it in the public release.
Beaufort says opening PDFs in Chrome is "safer" than doing so via an installed program, though users are free to alter this behaviour by right-clicking on a downloaded PDF and choosing the "Open with system viewer" option.
To be honest, I've never seen Chrome open PDFs in anything but its own viewer, but for those who prefer the likes of Foxit, Sumatra or Adobe's own software, you might want to keep an eye on this next time Chrome updates.