BackgroundTicks are important ectoparasites of horses that can affect animal welfare and vector several infectious, including zoonotic, diseases. In order to investigate the species distribution, epidemiology and seasonal dynamics of ticks infesting horses in Israel, 3267 ticks were collected from 396 horses in 24 farms across the country from July 2014 to June 2015.ResultsTicks were found on 50% of the farms and on 25% of the horses, with Hyalomma being the most prevalent genus (70% of ticks). Pasture was the most prominent risk factor for tick infestation (99% of ticks, P < 0.001), and is represented here by two areas with a Mediterranean climate that differ in their environmental characteristics: the Golan Heights (GH, 74% of ticks); and the Carmel mountain ridge (CMR, 24%). Although these two sites are less than 100 km apart, the composition of the tick populations infesting horses differed significantly between them. In GH the most abundant tick species was Hyalomma excavatum (P < 0.001), while in CMR it was Hyalomma marginatum (P < 0.001). The GH also hosted a more diverse tick fauna than the CMR, including Haemaphysalis parva (peaking in the autumn, P < 0.001) and Rhipicephalus turanicus (peaking in the spring, P < 0.001), which were not found at the other sites. A few Rhipicephalus bursa, Hyalomma rufipes and Hyalomma turanicum were also found on horses.ConclusionsThe current findings can be used in epidemiological studies assessing the risk of tick-borne equine diseases in the area. Further analysis is needed to determine the specific distribution and habitat preferences of each tick species.Electronic supplementary materialThe online version of this article (10.1186/s13071-018-3093-0) contains supplementary material, which is available to authorized users.