Anthocyanins may develop on the stem of pepper plants, often starting around joints. This is normal and nothing to worry about. The colour is often a dark shade of purple and may look black at a glance in certain cases. Hopefully your plant has nothing worse than this. Is it otherwise healthy-looking?

All my jalapeños did that last year. They all came out healthy. Think it might have just been a characteristic of those plants.

That is very common among pepper plants.

Take a look here

http://forums.gardenweb.com/discussions/3165767/jalapeno-plants-healthy-but-look-at-my-stems

from my experience purple/dark stems means the plant is getting lots of light.. not a bad thing i suppose.. it happens even growing indoors when they're intense light for lots of hours.

Thanks everyone. Very encouraging.

Yah, my plants all have a lot of black in the stems. I have gotten them outside on a few sunny warm days but mostly just the floro shop lights but they are on an 18 on 6 off schedule and they are doing quite well.

Black in stems is very common on peppers. At least the ones that I have ever grown. Here is a Carolina Reaper that I just repotted a few days ago. It's stem is mostly black except for the very bottom.