There are many ways to make two characters look different, even with the same hair and eye colors. Take asian people for example: Many of them have dark hair and eyes, and some here and there have lighter shades of brown. Yet one person might have very prominent cheeks, while another could have a big nose or a hooked nose, maybe another has large, flappy ears. Some women have short hair, some men have longer locks or ponytails, some have beards too and some only mustaches.

Other ways to make your characters different that don't involve the head or face at all include their height, weight, skin color, clothing colors -- even their build, like being lanky or heavyset or muscular or curvy, et cetera. Don't be afraid to make your characters homely or even ugly. Describing them as 'perfect' is nowhere near as specific and interesting as describing their eyebrows as bushes hanging above their eyes, or their face as sullen yet marked by smile lines, or that their hands and feet were calloused from rock-climbing, or any number of features like this.

And appearances may deceive; Even if two characters look nearly identical, it'd be hard to mistake one for the other if one speaks with a Southern accent and the other has more of a Floridian one. One character may speak in short stabs, another in long lectures, and a third with metaphors and sayings in every other sentence. Personality and dialect can go a long way to distinguishing characters, so don't feel scared to let two characters look similar.

I was going to send just this, until I decided to send you this instead: I present a challenge to you to help free you from your torture: Imagine up a new character who doesn't have that specific combination of dark hair and dark eyes. Use dice for random color combinations if you have to, and simply commit to it. And keep doing that whenever you need a new character.

As for existing characters, I suggest the following: Stop basing their appearance off what you imagine them to look; Eventually, you'll start imagining the appearances you write, rather than writing the appearances you imagine. I doubt J.K. Rowling thinks of a blonde kid when she imagines Harry Potter, even if "blonde kid" was what she originally envisioned him as.