Do you mean is it safe to use two different capacity batteries, such as a LG HG2 and a HB6 in a mod? The answer is a definite no.
Also, if the batteries were not bought at the same time together and are not married, then again the answer is no.
You need to buy two new batteries, of the same make and model, and keep them together to use in a dual 18650 mod.
EDIT: Hang on, your not even sure if one is an 18650? No way is this safe, buy two new batteries, it sounds like you just found these two somewhere.