had this same problem a few days ago. you might have downloaded the wrong version of pydev for your python version (2.7.5 or something is my python version, but i downloaded pydev for version 3.x.x)
1) uninstall your current version pydev
2) you have to install the correct version by using the "install new software", then uncheck the "show only newest software" or whatever it is. then select the version that matched your python version, and install :)
i had the same problem when installing on ubuntu 16.04 via the repository. this was because the version it installed was not compatible with the python plug-in from http://www.pydev.org/updates/
instead of using the older version of both eclipse and pydev, i uninstalled eclipse via the repository by first clicking the 'install' button, then when it immediately switched to 'uninstall' i clicked that.
i then went to: http://www.eclipse.org/ and downloaded the recommended gz file. i then unzipped it into my /opt directory. i deleted the file path info from the command below and dragged the file "eclipse-inst-linux64.tar.gz" into terminal so it had the full file path.
sudo tar -xf /path/to/file -c /opt
i then used nautilus to navigate to my /opt/eclipse-installer folder and double-clicked on the file: eclipse-inst
this ran the installer. i accepted the home directory recommendation. i accepted the offer to open eclipse.
in eclipse i went help --> market place and then took the option to install pydev from there.
now when i got to window --> preferences, the option pydev exists.
pydev is not meant to be installed through eclipse's marketplace. follow the instructions at http://pydev.org/manual_101_install.html. specifically this part
installing with the update site
note: instructions are targeted at eclipse 3.5 onwards
to install pydev and pydev extensions using the eclipse update manager, you need to use the help > install new software... menu (note that in older versions, this would be the 'find and install' menu).
so basically you have to install it using the "install new software" menu. it's explained in detail in pydev's own installation manual.
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