Eclispe uses its own SSH-Implementation, which does not respect your ~/.ssh/config and does not use the SSH agent.

This is bad when you want to use GIT via SSH from within Eclipse, have your keys loaded in the agent and a custom ssh config. There is a plugin, that allows Eclipse to access the agent. But there is a better solution; You can tell Eclipse to use the native SSH client, by1

export GIT_SSH=/usr/bin/ssh