The term arose in 19th century Britain. One of the by-products of the industrial revolution was a massive increase in the smoke and sulphur put into the atmosphere by factories, etc. When combined with fog, the result was totally different to the white fogs seen in rural areas - because of the dirty yellow-brown color, they were named "pea soupers".

These poisonous combinations of smoke and fog continued to occur until 1952, when a five-day "pea souper" over London is estimated to have caused 4,000 premature deaths through bronchitis, pneumonia, etc. Cold weather meant an increase in coal-burning, and meteorological conditions led to the pollutants being trapped at ground level. Subsequent changes in legislation phased out open coal fires, and "pea soupers" are now a thing of the past in Britain.

More background on the 1952 Great Smog:
http://news.bbc.co.uk/1/hi/england/2545759.stm