Three species of Brevipalpus mites are known potential vectors of the citrus leprosis virus (family Rhabdoviridae, genus Cyto- and Nucleorhabdovirus, CiLV). Species identification of these mites is difficult because of their small size and morphological similarities. The objective of this study was to develop an accurate and rapid molecular fingerprinting method for identifying B. phoenicis and B. californicus on Texas citrus. Iso-colonies of the two Brevipalpus species were cultured on immature citrus fruit and identified using a dichotomous key. Whole genome amplification was used to produce DNA template from single mites to identify the two species by amplified fragment length polymorphism and sequence-characterized amplified region (SCAR). Population dynamics of Brevipalpus were monitored in four citrus orchards during the 2007 growing season. Subsamples of mites were identified morphologically or by species-specific SCAR markers. Molecular fingerprinting was very efficient in identifying the two species of mites in subsamples, even in cases where the morphological identification did not discriminate between species. Brevipalpus spp. density per fruit was significantly affected by the host plant species, with sweet orange fruit hosting significantly higher density than grapefruit, Citrus x paradisi Macfad. The percentage of fruit infested with Brevipalpus mites varied significantly with time but not with host plant and the host plant by sampling date interaction. Comparison of molecular fingerprinting and morphological identification provided a high percentage of match >85% between the two methods, suggesting that molecular fingerprinting could facilitate studies on population dynamics of Brevipalpus in citrus.