Mucus in the back of your throat can be coming from one of two different places. First, this mucus could be coming from your lungs. If you are a smoker or if you have severe allergies, you could be making a lot of mucus in your lungs that is then getting coughed up.If you don't find yourself coughing all that much throughout the day, then the mucus is probably not coming from your lungs.f you are having a significant amount of nasal drainage that is draining to the back of your throat, then this may be where your mucus is coming from. The most common cause of this type of thing is season allergies.