The difference between Jupiter and Zeus lies in their origins. Zeus is from Greek mythology, whereas Jupiter is from Roman mythology. They have numerous similarities, however, It is likely that Jupiter was inspired by Zeus.
Zeus and Jupiter are equivalents of each other but come from different ancient civilizations. Zeus, from Greek mythology, is king of the gods and ruler of the sky. He is often depicted as throwing lightning bolts and ruling storms. Jupiter, from ancient Roman mythology, is depicted and described in the very same way. Both are married to their sisters, and both are king of the set of gods created in their own branch of mythology.
Zeus is generally more popular and has many connections with the god that most modern-day Christians believe in, though he is still comparable to Jupiter. For instance, in the birth story of Jesus Christ, the Virgin Mary is impregnated by the holy spirit. In many Greek stories, Zeus impregnates a maiden, and the child grows up to do great things and eventually becomes a hero. Both Jupiter and Zeus are depicted as having very personal relationships with the human race, and both are connected to legendary floods that have wiped out humanity.