Both classes will help you gain strength and flexibility and will offer a lot of compliments to your running regiment. Yoga will give your body a completely balanced workout, which I think may be more beneficial in the long run. It depends exactly what you're looking for. I wrote this article a while ago and it outlines the benefits of both and differences between them. http://www.active.com/mindandbody/articles/Yoga_Versus_Pilates__Which_One_s_Right_for_You_.htm. Hope it helps!