It will be heard many times in class, “Breath through your nose!” There is good reason for this – both from a western and an eastern standpoint.
Western medicine offers a number of scientific reasons why breathing through the nose is superior to breathing through the mouth. Nasal breathing provides better air filtration than oral breathing due to its cleansing passage through the nostrils and sinuses. Additionally, the nasal passage warms the air as well as lubricates it so as to lessen further damage to the throat. You will notice a big, big difference between breathing through your nose or your mouth when training in the cold or when you have a sore throat or laryngitis.
Eastern medicine and most Chinese martial arts suggest breathing through the nose exclusively – although there are some styles that exhale through the mouth. There are a number of reasons for breathing through the nose. It is thought that the regulation of your internal energy (chi) can only be accomplished when your breath has been regulated properly via nasal breathing. Controlling your breath thru the nose when overly exhausted (such as holding stances for a very long time or doing a thousand kicks) or when excited is necessary to control your energy and avoid stomach cramps that often come from breathing through your mouth. This is particularly important in sparring or in an actual fight as nasal breathing assists in withstanding attacks to the abdomen. Should you get kicked in the stomach while breathing through your mouth, you are in for trouble. Whereas, breathing through your nose (with proper training) provides more protection.
You should still train with a congested nose due to sickness or allergies. Although it will be difficult, try your best to breath through your nose anyway. It may require focus and effort, but it is often the case that the congestion is gone by the end of class if you get lost in your training. If the congestion is too great, bow out of class to blow your nose and hurry back. Then, try again to focus on breathing through your nose.