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DNA was extracted from pools of Amblyomma americanum ticks collected from vegetation at two sites in Fort Leonard Wood, Missouri and tested for the presence of Borrelia spp. Two new methods were developed to detect Borrelia lonestari DNA by targeting the glycerophosphodiester phosphodiesterase (glpQ) gene. The first method detected B. lonestari DNA using a SYBR green I melting curve analysis of the PCR product obtained with glpQ gene primers. The second method, a glpQ TaqMan assay, detected and confirmed the presence of B. lonestari glpQ-specific sequences. Twenty-two of 95 tick pools collected at site A148 contained B. lonestari DNA. None of 19 pools from site A241 contained B. lonestari DNA. No B. burgdorferi sensu lato DNA was detected using a SYBR green I melting curve analysis of the PCR product obtained with outer surface protein A (ospA) primers. The overall B. lonestari infection prevalence (with 95% confidence interval) at site A148 was estimated using two algorithms: minimum infection rate 4.14% (2.45, 5.84) and maximum likelihood with correction 4.82% (3.11, 7.16). The merits of each are discussed. Sequencing of the entire B. lonestari glpQ and partial 16S rRNA genes revealed two genetic variants circulating in this population of A. americanum from Missouri.