Yes, you can install both from apt very easily. (Not true, as Indigo is not supported on 12.04. Thanks @ahendrix. See Edit2 below.) You select which you are using by sourcing the appropriate setup.bash file. Note that when you switch between ros distros, it is probably best not to put the source .../setup.bash in your .bashrc.
There is even some level of interoperability between the distros (i.e. running hydro and indigo nodes together with the same roscore), as long as the messages involved have not changed. Most notably the diagnostic messages have changed and thus anything involing robot dashboards will not work across distro.
Note that everything I wrote in the previous paragraph does not affect your ability to run hydro and indigo systems alongside each other with separate ros cores even on the same machine.
EDIT:
Yes, you can follow the instructions at http://wiki.ros.org/indigo/Installati... to install indigo on a machine where you have hydro installed.
Some steps are unnecessary since you did them already for your hydro install (e.g. "1.1 Configure your Ubuntu repositories", "1.3 Set up your keys", sudo rosdep init). Be careful in "1.6 Environment setup". You don't want to source both indigo and hydro setup files in your .bashrc. As noted above, it is probably best to not source either in your .bashrc but rather source them manually on each shell when needed. You might want to define your own bash aliases like source_hydro to make this more convenient.
EDIT2: as @ahendrix has rightfully pointed out, my answer is somewhat misleading since Indigo is in fact not officially supported on Ubuntu 12.04 and therefore has no debs to install from apt (see Target Platforms ). The gist of the answer -- that multiple versions of ROS can be installed and used on the same system -- remains true. Of course the prerequisite is that each of the version is installable separately on that system in the first place. E.g. on OS X I have both hydro and indigo installed (from source). You might achieve the same on Ubuntu 12.04 by installing hydro from apt and indigo from source ( http://wiki.ros.org/indigo/Installati... ).
