The largest extinction in earth's history occurred at the Permo-Triassic boundary (end of the Permian, which marked the beginning of the Triassic).  This extinction event affected the invertebrates the greatest.  At the time, therapsids and pelycosaurs were the most abundant reptiles, and this was when acanthodians, placoderms, and pelycosaurs became extinct.  In the Permian gymnosperms (seedless plants) were diverse and abundant, the single continent of Pangaea was formed, and the Alleghenian and Hercynian orogenies occurred (mountain building).

Some resources for the evidence and theories as to why this extinction occurred:

http://palaeo.gly.bris.ac.uk/Palaeofiles/Permian/intro.html

http://www.priweb.org/ed/ICTHOL/ICTHOLrp/72rp.htm

http://www.nationalgeographic.com/ngm/0009/feature4/

http://www.uky.edu/KGS/education/EndPermian.htm

http://www.space.com/scienceastronomy/solarsystem/permian_impact_010829.html

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