Waking up in the morning with thick sputum like jelly may be caused by sputum that is too sticky, and also needs to be combined with the color of the sputum to determine. 1. Generally speaking, patients with Klebsiella infection will cough up brick-red jelly-like sputum; coughing up yellow pus sputum may be a common bacterial infection such as Staphylococcus aureus; coughing up green sputum may be caused by Pseudomonas aeruginosa infection; if the sputum is rust-colored, it may be Streptococcus pneumoniae infection. If you wake up in the morning with thick, jelly-like sputum, you should seek medical attention and ask your doctor to take care of it.