A field survey was conducted in 2001 to evaluate resistance to pyrethroid and organophosphate (OP) insecticides on horn flies, Hematobia irritans irritans (L.), from seven ranches in the state of Tamaulipas, Mexico, and from three locations in central Texas. Filter papers impregnated with either technical permethrin or diazinon were used to measure the levels of resistance to pyrethroids and OPs. A multiplex polymerase chain reaction (PCR) assay was used on individual horn flies from these field populations to detect the presence of the kdr and super-kdr alleles associated with pyrethroid resistance, and a mutated αE7 esterase allele associated with OP resistance. Relative to a susceptible laboratory (Kerrville) strain, horn flies from Mexico exhibited 5.1- to 28.3-fold resistance to permethrin at the LC₅₀, and 23.8- to 136-fold resistance at the LC₉₀. Horn flies from Texas ranches exhibited only two- to five-fold resistance. All field populations of the horn fly were highly susceptible to diazinon, and no mutant αE7 esterase alleles were detected. The super-kdr allele was found only in a single fly from a ranch in Mexico. Results of PCR assays showed that the kdr allele was present at various frequencies in field populations of horn flies. A gender-related bias in distribution of kdr genotypes was found in horn flies from Mexico, but not in horn flies from Texas. The overall kdr allelic frequencies in horn flies from Mexico were 23.2–37.8% higher in females than in males. Regression analysis revealed a significant correlation between kdr allelic frequencies and the levels of knockdown resistance to permethrin among the horn fly populations studied. The results validate the role of the PCR-based molecular assay as a diagnostic tool in monitoring resistance to pyrethroids and also provide useful information on population genetics of horn fly resistance to pyrethroids and OPs.