Philophthalmosis is a zoonotic disease associated largely with the spread of the invasive freshwater snail Melanoides tuberculata, serving as an intermediate host. Here we examined Philophthalmus gralli focal fenced infection site reported recently as being associated with Tinamus major and M. tuberculata in Alajuela, Costa Rica. Removal of the definitive hosts allowed us to address also the long-term survival strategy of the parasite. Initially, the snail intermediate hosts displayed high prevalence of P. gralli infection across all its age cohorts. Two years following the removal of definitive hosts, the infection rate decreased by one order of magnitude, while the snails aging less than one year displayed zero infection prevalence. Additionally, phylogenetic analysis of mitochondrial (ND1) and nuclear (ITS1, ITS2) DNA loci revealed negligible intrasite DNA variability of the specimens obtained at the study site in Costa Rica (but not of those obtained earlier in Peru or New Zealand), supporting strongly the hypothesis on focal origin of the infection. The observed dynamics of infection suggests the explanation for the high variability in P. gralli prevalence in intermediate hosts experienced worldwide. We noticed that the reports claiming >20% prevalence of M. tuberculata infection by P. gralli originated exclusively from foci with known eye infection of the definitive hosts, while the P. gralli infection penetrance <2% is typically associated with sites, where the infection of definitive hosts was not observed, suggesting that the infected definitive hosts were present onsite only in the past, or were present only at a site upstream or downstream of the respective sampling site. Thus, this is the first evidence on the possible persistence of eye-trematode infection site for over two years following the last confirmed outbreak in its adult hosts.