Whitefly-transmitted geminiviruses (Subgroup ΙΠ, Geminiviridae) have long recognized as pathogens of weed species and bean crops in Puerto Rico, and were recently shown to cause diseases of tomato. At least five symptoms phenotypes were associated with infected tomato in P.R. during 1991-1996. Geminivirus etiology was demonstrated by whitefly transmission and polymerase chain reaction (PCR) detection using subgroup III universal PCR primers. At least three distinct genotypes were discerned in infected tomato based upon comparison of key virus sequences with those of well-characterized subgroup III viruses. Each virus genotype has a unique experimental host range and causes differential symptoms in diagnostic test species. The precise relationships between P.R. viruses that are indigenous to weed hosts and those found in bean and tomato are under investigation in order to identify the most economically important viruses to target for resistance efforts, to map their distribution in host plants, and to evaluate the potential for recombination or reassortment in the formation of new and emerging geminiviruses.