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The bacterium  Xylella fastidiosa  is a plant pathogen with a history of economically damaging introductions of subspecies to regions where its other subspecies are native. Genetic evidence is presented demonstrating the introduction of two new taxa into Central America and their introgression into the native subspecies,  X. fastidiosa  subsp.  fastidiosa . The data are from 10 genetic outliers detected by multilocus sequence typing (MLST) of isolates from Costa Rica. Six (five from oleander, one from coffee) defined a new sequence type (ST53) that carried alleles at six of the eight loci sequenced (five of the seven MLST loci) diagnostic of the South American subspecies  Xylella fastidiosa  subsp.  pauca  which causes two economically damaging plant diseases, citrus variegated chlorosis and coffee leaf scorch. The two remaining loci of ST53 carried alleles from what appears to be a new South American form of  X. fastidiosa . Four isolates, classified as  X. fastidiosa  subsp.  fastidiosa , showed a low level of introgression of non-native DNA. One grapevine isolate showed introgression of an allele from  X. fastidiosa  subsp.  pauca  while the other three (from citrus and coffee) showed introgression of an allele with similar ancestry to the alleles of unknown origin in ST53. The presence of  X. fastidiosa  subsp.  pauca  in Central America is troubling given its disease potential, and establishes another route for the introduction of this economically damaging subspecies into the US or elsewhere, a threat potentially compounded by the presence of a previously unknown form of  X. fastidiosa .

The Complex Biogeography of the Plant Pathogen Xylella fastidiosa: Genetic Evidence of Introductions and Subspecific Introgression in Central America