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Based on known data sets and maximum entropy distribution data of fern and lycopod species registered in the Yucatan Peninsula, track and parsimony analyses were undertaken to evaluate the contribution of these groups to the establishment of biogeographical relationships of the peninsula with other areas. The resulting generalized tracks clearly agree with the geological origin of the peninsula and the previously recognized relationship with the Greater Antilles is not supported for ferns and lycopods. Instead, a Central American generalized track connects the Yucatan Peninsula with south-eastern Mexico and Central America. Floristically, the peninsula harbours 66 species of ferns and lycopods. Seven are registered for the first time in the Yucatan Peninsula and one is a new species for Mexico. These species do not follow the latitudinal pattern expected if ecological factors, such as humidity and rainfall, were the most important in determining their distributions. Groups of areas recognized with parsimony analysis of endemicity could not be defined as provinces as a result of the lack of endemic species. Nevertheless, a regionalization scheme based on maximum entropy distribution data and supported by track analyses is proposed. Two separate districts are recognized within the Yucatan Peninsula: arid/dry Yucatan in the north and El Peten (humid) in the south. (C) 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 98, 775-786.