One of the techniques that zooarchaeologists use is close attention to taphonomy. This includes studying how items are buried and deposited at the site in question, what the conditions are that aid in the preservation of these items, and how these items get destroyed. Then they interpret that information.
Another technique that zooarchaeologists use is lab analysis. This analysis can include comparing the skeletons found on site with already identified animal skeletons. This not only helps to identify what the animal is, but also whether the animal was domesticated or not.
Yet another technique that zooarchaeologists use is quantification. They make interpretations based on the number and size of the bones. These interpretations include how important different animals might have been to the diet.