Similarity in parasite community composition often decreases with both increasing geographic distance and environmental dissimilarity between localities, though it is unknown whether similarity in local abundance of selected parasite species follows similar rules. We tested this using data on metazoan parasites in 126 stickleback (Gasterosteus aculeatus) populations, with locations from Eurasia, eastern North America, and western North America treated separately. Similarity values were regressed against pairwise distances between localities; after correcting for distance, the effect of environmental dissimilarity was assessed by splitting similarity values into those between pairs of localities with either similar, moderately different or very different salinity (freshwater, marine or brackish). For selected parasite species, pairwise similarity in abundance (mean no. parasites per host) were computed across all localities, and treated as above. Similarity in parasite community composition decreased with increasing distance between localities in all three geographic regions. A significant effect of environmental difference was found in all regions: for a given distance between two sites, their parasite communities were more similar if they were of the same salinity. Slopes for distance decay in similarity were consistently higher for eastern North America than for Eurasia. Among the 12 parasite species for which sufficient data were available, only 4 showed the expected relationship, i.e. the greater the geographical separation between host populations, the greater the difference in parasite abundance; also, significant effects of environmental differences in salinity were only found for 3 of these species. Our findings show that parasite communities of sticklebacks are structured by geographical distance and local salinity conditions. The results indicate that strong effects at the community level do not translate into corresponding effects at the population level, suggesting that parasite dispersal and population dynamics are controlled by different processes.