Methane (CH₄) is the second most important greenhouse gas. CH₄ is more potent than CO₂ because the radiative forcing produced per molecule is greater. In addition, the infrared window is less saturated in the range of wavelengths of radiation absorbed by CH₄, so more molecules may fill in the region. However, CH₄ exists in far lower concentrations than CO₂ in the atmosphere, and its concentrations by volume in the atmosphere are generally measured in parts per billion (ppb) rather than ppm. CH₄ also has a considerably shorter residence time in the atmosphere than CO₂ (the residence time for CH₄ is roughly 10 years, compared with hundreds of years for CO₂).

Natural sources of methane include tropical and northern wetlands, methane-oxidizing bacteria that feed on organic material consumed by termites, volcanoes, seepage vents of the seafloor in regions rich with organic sediment, and methane hydrates trapped along the continental shelves of the oceans and in polar permafrost. The primary natural sink for methane is the atmosphere itself, as methane reacts readily with the hydroxyl radical (OH⁻) within the troposphere to form CO₂ and water vapour (H₂O). When CH₄ reaches the stratosphere, it is destroyed. Another natural sink is soil, where methane is oxidized by bacteria.

As with CO₂, human activity is increasing the CH₄ concentration faster than it can be offset by natural sinks. Anthropogenic sources currently account for approximately 70 percent of total annual emissions, leading to substantial increases in concentration over time. The major anthropogenic sources of atmospheric CH₄ are rice cultivation, livestock farming, the burning of coal and natural gas, the combustion of biomass, and the decomposition of organic matter in landfills. Future trends are particularly difficult to anticipate. This is in part due to an incomplete understanding of the climate feedbacks associated with CH₄ emissions. In addition, as human populations grow, it is difficult to predict how possible changes in livestock raising, rice cultivation, and energy use will influence CH₄ emissions.

It is believed that a sudden increase in the concentration of methane in the atmosphere was responsible for a warming event that raised average global temperatures by 4–8 °C (7.2–14.4 °F) over a few thousand years during the so-called Paleocene-Eocene Thermal Maximum (PETM). This episode took place roughly 55 million years ago, and the rise in CH₄ appears to have been related to a massive volcanic eruption that interacted with methane-containing flood deposits. As a result, large amounts of gaseous CH₄ were injected into the atmosphere. It is difficult to know precisely how high these concentrations were or how long they persisted. At very high concentrations, residence times of CH₄ in the atmosphere can become much greater than the nominal 10-year residence time that applies today. Nevertheless, it is likely that these concentrations reached several ppm during the PETM.

Methane concentrations also varied over a smaller range (between roughly 350 and 800 ppb) in association with the Pleistocene ice age cycles. Preindustrial levels of CH₄ in the atmosphere were approximately 700 ppb, whereas levels exceeded 1,867 ppb in late 2018. (These concentrations are well above the natural levels observed for at least the past 650,000 years.) The net radiative forcing by anthropogenic CH₄ emissions is approximately 0.5 watt per square metre—or roughly one-third the radiative forcing of CO₂.

Surface-level ozone

The next most significant greenhouse gas is surface, or low-level, ozone (O₃). Surface O₃ is a result of air pollution; it must be distinguished from naturally occurring stratospheric O₃, which has a very different role in the planetary radiation balance. The primary natural source of surface O₃ is the subsidence of stratospheric O₃ from the upper atmosphere. In contrast, the primary anthropogenic source of surface O₃ is photochemical reactions involving the atmospheric pollutant carbon monoxide (CO). The best estimates of the natural concentration of surface O₃ are 10 ppb, and the net radiative forcing due to anthropogenic emissions of surface O₃ is approximately 0.35 watt per square metre. Ozone concentrations can rise to unhealthy levels (that is, conditions where concentrations meet or exceed 70 ppb for eight hours or longer) in cities prone to photochemical smog.

Nitrous oxides and fluorinated gases

Additional trace gases produced by industrial activity that have greenhouse properties include nitrous oxide (N₂O) and fluorinated gases (halocarbons), the latter including CFCs, sulfur hexafluoride, hydrofluorocarbons (HFCs), and perfluorocarbons (PFCs). Nitrous oxide is responsible for 0.16 watt per square metre radiative forcing, while fluorinated gases are collectively responsible for 0.34 watt per square metre. Nitrous oxides have small background concentrations due to natural biological reactions in soil and water, whereas the fluorinated gases owe their existence almost entirely to industrial sources.