The biogeography of host-parasite dynamics is an area that has received little attention in studies of island ecology. While a few studies have shed insight on patterns of parasitism in insular host populations, more empirical evidence is needed to ascertain how isolation impacts parasites. Biogeography generally theorizes that the physical size of islands and the duration of each island’s isolation can be driving geographic factors controlling species interactions and populations dynamics. To test this, we assessed the effect of island structure and population isolation on the endemic insular lizard Podarcis erhardii and its native hemogregarine parasite (Apicomplexa: Adeleorina) in the Cyclades (Aegean Sea). We analyzed the relationships of prevalence and parasitemia of hemogregarine infection with several factors concerning the island (size, time of isolation, spatial isolation, population density) and host (body size) levels using regression and structural equation models, respectively. Regressions indicate that islands with greater host density and islands which have been isolated for shorter timespans tend to have higher hemogregarine prevalences; structural equation models suggest a similar pattern for parasitemia. We hypothesize this may be driven by insular density compensation. Hosts on islands that are more temporally and spatially isolated also tend to have higher prevalence and parasitemia of hemogregarines. Our results indicate that island area, island isolation, and host population density are likely to be significant drivers of changes in host-parasite interactions in fragmented populations.