This could be what has been termed "Black Skin disease" or scientifically known as Alopecia X. Mostly it occurs in pomeranians but I am not surpised that it could be possibly happening to your chihuahua seeing that they are also small breeds. BSD occurs more in males than females and is believed to be genetic. Scientists don't know exactly why it happens but believe it is something in the X chromosome. Seems to be associated with a hormonal imbalance, which is why the first treatment is spaying of neutering, in which case, he is already taken care of in that area.

Some dogs with BSD begin to have a funky odor and start loosing patches of hair. They can also develop a waxy feel to their skin. However, of course depending on the severity, some dogs odor are eliminated easily with regular baths with a medicated shampoo. If the dogs skin begins to flake a medicated moisturizing shampoo will help. At this point, all that can be done for BSD is control, there presently is no cure. Melatonin is used by most vets in the cases that are accompanied with hair loss. Because some dogs don't respond to this medication, others such as prednisone or ketoconazole are often used.BSD is frustrating and will be for quite some time but research is on-going on this disease.

Now, before we decide this is in fact BSD. You should first go to the doctor and rule out things lik thyroid deficiencies, bacterial infections (dark spots can be contributed to bacteria or even parasites or allergies (food, flea dirt, etc). You should consult your vet in order to administer these tests so that we can treat accordingly.

Because I myself own a pomeranian (typically prone to BSD but chows, chihuahuas, cocker spainiels and others can get the disease), I tend to frequent alot of the pom sites. I also add alot of to my bookmarks...it just so happens that I have a URL for you that you might be interested in. It is different people who have canines who have the disease and describe their dogs issues and shampoos and remedies they have tried. It may be beneficial for you to take a look at it so that you can either confirm or rule out BSD and whether you should take your dog to the vet sooner than later.

http://www.faqs.org/qa/qa-1677.html

I hope I have helped. Let me know if I can do anything else for you. :) Would you mind keeping me updated on his situation? Thanks a bunch.