We are seeing icy clouds of gases moving at high speeds in the atmosphere. Jupiter's atmosphere is composed of about 90% hydrogen and 10 %helium. There are only minute traces (0.07%) of methane (CH3), water, ammonia, and rock dust.
Jupiter's "atmosphere" is kind of a misleading choice of words since the planet is composed of gas. What we are referring to here is the part of that gas planet that we visualize and know something about. the atmosphere of Jupiter is very complex. Jupiter holds clues to many of the mysteries of the early solar system. About 4.5 billion years ago, when the solar system formed out of a swirling mass of gases and dust called the solar nebula, Jupiter's core probably began as a solid mass of ice and rock about 15 times the bulk of Earth. The ice content of Jupiter's mass was high because it formed in the colder outer region of the solar system, where the nebula contained a lot of ice particles, principally water and methane. Probably because icy masses can adhere and compress into a single large body faster than plain rock can, the outer planets formed their cores before the rocky inner planets did. The gravity of the large icy cores of Jupiter and Saturn attracted most of the light hydrogen and helium gas in the nebula, and it is these gasses that we find dominating their atmospheres today. Jupiter, the innermost of the icy giants, "grew" the largest atmosphere. In fact, the face of Jupiter that we see is really just the top of its atmosphere. What goes on inside is even more intriguing.