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I had white flies on some of the other plants, but they're dead now... I used some 'organic-safe' insecticide. The brown spots are just on the top of the leaf. From the bottom you can only see them if you hold it to the light, and its just where the leaf was less-transparent.

Thanks! I thought it was something like that too, since before those spots developed I had them inside under CFL's. Though they aren't in direct sunlight because of the greenhouse... hopefully someone more intelligent about these things will read this post soon :)

Hey there, I'm a new comer to this whole game and have started some different chili's and such in hydroponics outside, in a greenhouse. I've found that all of my chilis (bell pepper, jalapeno, tabasco, cherry peppers) all have many brown spots on their leaves. I also have some okra in the tank...