It sounds like blossom end rot. Here's a link with a picture and the causes and solutions.
http://ohioline.osu.edu/hyg-fact/3000/3117.html

It does sound like blossom end rot (BER). What I have found to cause it in my own garden and through a few years of experience is watering. Granted, I have only been gardening for 4 years here in AZ, but that's 8 growing seasons.

Before I learned how to properly water my beds and containers, I had scads of BER - on both tomatoes and peppers. Now, I water so that the soil stays semi-moist most of the time. It means that I water more frequently but use less water. I have 0.70 OD drip lines spaced every foot with 2GPM emitters spaced every foot down the lines on both sides. I run them 15 minutes twice a day. When the temps get up over 100, I will increase this three times per day. My garden tends to thrive with this watering regimen.

Some people swear that mulching will prevent water evaporation and lead to less watering and hence less BER, but I tried this last year without much success.

In my experience, I am getting less BER as time goes on. However, sometimes, BER just seems to show up. I found this to be true for earlier tomatoes. Eventually, the plant just seems to grow out of it and the later tomatoes turn out normal.

Hope this helps.

Brian

It's blossom end rot and is caused by a lack of calcium in the fruit...not necessarily the soil. If you're planting in amended native soil, most likely it was caused by stress as a result of inconsistent watering which would make it difficult for the plant to absorb calcium. Also, roma varieties are very susceptible to BER for some reason. I grew 34 plants last year, 2 were San Marzano....only those 2 had BER problems.

The link that agility mom posted is more comprehensive but DO NOT add lime as they suggest...that is advice for ohio soils, not arizona soils.

Thanks everyone so much for the answer. I will watch it for a while and see whats what. I am already mulched with alfalfa hay but have been trying to water deeply and less frequently. THe twice daily watering just wouldnt work for me as I have to use a hose to water and I work 12 hour shifts. I have lots of tomatoes coming on so hope that the plants will "grow out of it"

I would watch mulching with alfalfa hay. I buy the best for my horses but it still has weeds in it and they will come up in your garden.

i had BER earlier in the season, my tomatoes are finally normal with only a couple left that have it. it freaked me out, but i was happy to harvest my first normal one. all the other green fruits look good. probably, your plant will grow out of it.

Keep the moisture EVEN. Lack of calcium is seldom a problem for a desert soil, but it takes consistent soil moisture and a heavy mulch to minimize BER.

By the way, it is ?NOT a mold or harmful to humans - I just trim them off and eat the rest of the tomato.

doesn't alfalfa hay contain quite a bit of nitrogen? I thought they even use alfalfa as a fertilizer. adding more nitrogen in a situation with BER will make the situation worse because nitrogen makes it harder for the plant to take up calcium from the soil. There are some foliar feeds that are supposed to help give the plant calcium directly through the leaves for a little boost. Overall I think the solution is to do things to improve your soil in the long run and to water evenly. Improved soil, will hold water better, the hummus from compost increases the ability of roots to take up nutrients, so everybody is happy.

Looks like my tomatoes are not immune. So far its only showing up on a few of the Cherokee Purple's. Everything else seams to be alright. I did a quick soil check and found some places that are dry as bone in the raised bed. Ive decided to add a few more drip lines. Hope it works.

I havent had any more tomatoes with the BER so hopefully it is gone for good. Thanks for everyone's input.
And by the way, I have only raised beds filled with compost and potting soil. The alfalfa mulch definitely helps with keeping cool, and I want the extra nitrogen. Not all of the compost was completely finished when I started and filled the bed (stock tank, in this case).