From what I have read here could it be citrus rust mite?

http://www.mastergardenerssandiego.org/faq/item.php?ID=35

Googling citrus rust mite and looking at the images looks similar to your image.

Andrew, honestly, I have no idea but in case some of the experts see this question, they might want to know- where do you live?

I live in Tampa, FL.

BaconEater - Citrus rust mite was the first thing I came up with googling. The thing I had read said I should be able to see them with a magnifying glass, but I couldn't. The link you provided says 20x mag, though, so maybe it is them, after all. Although, the google images match the discoloration, but don't seem to have the scarring. So maybe I am dealing with two things.

You won't see the mites now; they affected the fruit when it was very small. With any luck, the inside should still be fine. Look for them next year when you see new, tender growth; check every day with a 10X loupe, especially on the underside of the leaves; and when you see them, treat with a miticide. I use Bayer Oberon; but I don't know if that is available where you are.

Evan

One of my Ponderosa Lemons has markings like that. The other ones on the tree doesn't have it. It probably got the mite damage when it was young, but the others didn't as I was more careful with spraying my trees as the summer went on. The inside of the fruit will probably be ok.

Cory

I have a couple of comments that may help. First, I recall seeing Satsuma oranges that had a very dark peel like that at a nearby orchard. They gave me some of the oranges since they didn't want to sell them like that. They were VERY good and maybe even sweeter than the others...so try them when they show signs of being ripe...some orange in there somewhere.

Second, I have Ponderosa lemons and grackles and other birds will sometimes scrape on the peel for the oil when the fruit is young. It also causes a similar kind of scarring but not the black coloration you see on the rest of your fruit. In that case, the scaring is unsightly and ruins that part of the zest but the fruit is good otherwise.

I have a fair amount of rust mite damage on my Satsuma and Orange trees. The fruit with orange color still visible is good. BG the fruit in which the damage is more advanced and the entire peel is discolored wasn't good at all.

Belated thanks everybody. Tried one today that seemed not too damaged and colored more or less correctly. I don't think it was ready yet, barely any taste to it. There was a but of brown discoloration at the stem end of the actual fruit, not sure if that's a problem.