The possibility of recombination within tick-borne flaviviruses was raised by Twiddy et al. [14] , but given the low amount of genetic variation in this group, they pointed out that detection would prove difficult. A recent report [16] would indicate that tickborne flaviviruses have the potential to obtain and spread advantageous traits, and to remove deleterious genes [43] by homologous recombination. Alas, re-analysis of the published data did not recover that signal using a more accurate alignment method and more stringent detection conditions, but found evidences for a different event. Therefore our study shows for the first time that demonstrable recombination (that is, with sufficient statistical support and with strong phylogenetic evidences) has occurred in the mammalian tick-borne flavivirus group.