One suggests the decline was caused by greater commercial use of natural gas, the other that increased use in Asia of artificial fertiliser was responsible.
Both studies agree that human activities are the key element.
And there are suggestions that methane levels are now on the rise again.
Methane is regarded as one of the most potent greenhouse gases, trapping over 20 times more atmospheric heat than carbon dioxide.
Since the start of the industrial revolution, levels of methane in the atmosphere have more than doubled from a wide variety of sources, including energy production, the burning of forests, and increased numbers of cattle and sheep.
But between 1980 and the turn of the millennium, the growth rate reduced substantially, leaving scientists puzzled as to the cause.
Now, two teams of researchers have arrived at two very different conclusions for the decline. The first study was led by Dr Murat Aydin from the University of California, Irvine.
"We went after ethane - it's another hydrocarbon similar to methane, it has common sources, but is easier to trace. We determined what ethane did during the second half of the 20th century using ancient air that we collected at polar ice sheets.
"We think the trend we see in methane is best explained by dramatic changes in emissions linked to fossil fuel production and use which seem to have declined in the 1980s and 1990s.
Efficiency drive
Dr Murat is at pains to emphasise that economic efficiency played a critical part.
"Methane became economically valuable only during the second half of the 20th Century. We think this had a role in it. We're not suggesting we used less fossil fuel, but because we were more careful about capturing the natural gas and using it as an energy resource, emissions of these gases into the atmosphere declined at the end of the 20th Century."
However another team of researchers from the same department in the same university came to different conclusions using a different method of measuring methane.
The second team looked at different chemical signals of methane from both fossil fuels and from microbes active in wetlands and rice paddies.
Traditionally rice farmers have used organic manure which contains high levels of methane. By using artificial fertilisers, the farmers have considerably reduced this amount.
"Approximately half of the decrease in methane can be explained by reduced emissions from rice agriculture in Asia associated with increases in fertiliser application and reductions in water use," says the lead author Dr Fuu Ming Kai.
Fertilisers are believed to enhance the ability of some bacteria to consume methane that originates in the soils.
One or the other?
However, the second team found no evidence that the decline was caused by more efficient use of fossil fuels.
This has puzzled Dr Paul Fraser, an expert in methane emissions with the Centre for Australian Weather and Climate Research. He says both papers are plausible. But he is concerned that the second team may have been too quick to dismiss the idea that increased use of natural gas may have played a part.
"The authors may be correct but from the data shown it is not unequivocal that there could not also be a fossil methane contribution to the declining methane sources," he said.
However he says he would not be surprised if in the long term both explanations are significant in explaining the decline.
Climate sceptics who think that natural factors and not human activities play a more important role in temperature rise might take comfort from the lack of certainty in these papers - but according to Dr Murat Aydin this would be a mistake.
"I think both studies are actually suggesting that human activities are playing a very important role in determining the methane levels in the atmosphere," he explained.
As we use more and more fossil fuels, you can be sure it will start creeping up again slowly, I think it demonstrates pretty clearly that human activities have direct and pretty profound impacts on the levels of these gases in the atmosphere."