How do I change the unreadable dark blue color Cygwin uses for directories?

If you're using MinTTY (which you almost certainly are, unless you know you're doing something special), the easiest method is to change your MinTTY settings. You can do this by editing your ~/.minttyrc file.

Try running the below, then restarting MinTTY:

echo 'Blue=127,127,255' >> ~/.minttyrc
echo 'BoldBlue=191,191,255' >> ~/.minttyrc

This will work for everywhere that blue colour turns up, not just in the results from ls.

You probably get the colors from ls itself. You get this from invoking it as ls --color. You can either disable this alias, or you can change the colors. I find the colors useful, so I change the colors.

There are defaults, but you can override these by use of the LS_COLORS environment variable. You can set this manually, or you can use the tool dircolors to help you.

There is also a command line option --option that allows you to change colours

E.g. The following changes the blue to something more readable

C:\cygwin\bin\mintty.exe --option Blue=128,128,192 -i /Cygwin-Terminal.ico -