Combine beans and water in a large pot. Bring to a boil, reduce heat, and simmer for 3 hours. Add more water if necessary while beans are cooking.
In a large skillet, cook bacon over medium heat until it is beginning to brown. Stir in onion, and continue cooking until onion is tender. Stir in tomato, and jalapeno, and cook for 2 to 3 minutes. Remove from heat, and stir in cilantro.
Stir bacon and onion mixture into the beans, and continue cooking for 1 hour, or until beans are soft.
