BACKGROUND: Acaricide resistance is a central problem for the control of the cattle tick Rhipicephalus microplus. The physiological effects and phenotypes of the mutations that cause acaricide resistance are not always well understood or characterized. Single nucleotide polymorphisms (SNPs) that confer cypermethrin knockdown resistance (kdr) have been reported in R. microplus. These SNPs have been associated and correlated with pyrethroid resistance although there is no direct physiological evidence that their presence does confer kdr in this organism. METHODS: Resistant and susceptible strain resistance profiles were obtained using the larval packet discriminating dose assay. The relevant genomic regions of the para-sodium channel were amplified using standard PCR; SNPs were detected by sequencing the corresponding amplicons. Ovary response to cypermethrin exposure/treatment was evaluated using videometrical analysis. RESULTS: We found that the pyrethroid resistance trait is stable in a resistant reference strain after years without selection, suggesting that the resistance conferring mutations are fixed in the population. In this strain, a change in the structure of the pre-synaptic para-sodium channel caused by the G184C, the C190A and the T2134A SNPs appears to confer resistance. These mutations are absent in the susceptible strain used as control. We demonstrate that cypermethrin blocks ovary contraction in cypermethrin-susceptible ticks. We also show that ovaries from organisms that carry the kdr associated SNPs still contract at cypermethrin concentrations that completely block ovary contraction in the susceptible strain. The configuration of the experimental system excludes a xenobiotic detoxification mechanism. CONCLUSIONS: This is the first report that presents physiological evidence that the presence of the G184C, the C190A, and the T2134A mutations in the para-sodium channel correlates with maintaining muscle contractility in R. microplus exposed to cypermethrin. These SNPs may confer cypermethrin resistance in this organism by avoiding presynaptic blockage, inhibiting the flaccid muscle paralysis characteristic of this acaricide. The videometric assay that we previously validated can be used to detect more rapidly than other assays that involve larval mortality kdr-like cypermethrin resistant tick strains, permitting to directly assay adult pre-engorged females after they are collected on the field without waiting until eggs are laid and larvae eclose.