Jupiter's atmosphere is high about 1000 km, and it is mostly made up of hydrogen (75.5%) and helium (23.8%), and from compounds such as methane, ammonia, water vapor, etc. The other atoms occur as impurities. Observed atoms of carbon, nitrogen and sulfur are the remains of the meteor and comet matter which attracted with strong gravity often falls on Jupiter. Data from the "Galileo" showed that oxygen is much less than expected (less than the sun). Pressure, temperature and density growth toward the center, and at a depth of 10 000 km below the cloud tops, density of the atmosphere grow to the density of water. On the level with a pressure of 150 millibars is inversion layer, the warmer the area above the cooler, as it exists in Earth's stratosphere.
Jupiter's atmosphere in the upper part is thermosphere, the temperature climbs to large amounts and therefore in it occurs layers of ions (the ionosphere), clouds hover in the lower atmosphere, in the troposphere.
As the details of the long distance is not well observed, cloudy layers seem to be very monotonous. Jupiter's atmosphere is subject to the same physical rules as the Earth's atmosphere or other planet. As the clouds consist of droplets and ice crystals, conclusion is that clouds occurring at an altitude where there is a substance that may drain and froze. Classical distribution of Jupiter's atmosphere by the amount taken to be the topmost layer consists of the ammonia crystal clouds (NH3), the lower layer of ammonium hydro-sulfide (NH4SH), and even lower clouds of water droplets and crystals. Ammonium clouds are blue-white and distributed in stripes - an observer on the Earth called them zones. The clouds of ammonium hydro-sulfide are yellow-orange and are spread as a continuous layer, we see them between the zones and call them bands. Here the temperature is too low to water drained. Water clouds can be under continuous layer of clouds, and that means invisible.
In cloudy layers are located clearings, areas of different temperatures. The hypothesis that Jupiter's atmosphere is not uniform is set, but there are large local differences, and probe was passed precisely the area that was warmer and without water vapor. In places deeper than where the pressure is 0.5 bars, atmosphere is very well blended. This is a consequence of heat that is transferred from the interior convection (mixing of gas particles).