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Background  Within the last 25 years, after the introduction of the swimbladder nematode  Anguillicoloides  crassus from East-Asia to Europe, a body of work has aggregated on the host parasite interactions in the acquired host  Anguilla anguilla . Despite the emerging evolutionary interest there is still a lack of knowledge about host parasite relations of  A. crassus  in its natural host  Anguilla japonica . We examined the  Anguillicoloides  infections of wild-caught Japanese eels as well as from aquacultured specimens in Taiwan with respect to the fate of migratory L3 larvae and performed infection experiments with Japanese eels.    Results  Inside the intestinal wall of cultured eels, where the infective pressure was higher than among wild eels, we found large numbers of granuloma-like cysts. In a few eels these cysts contained nematodes still recognizable as L3 larvae of  A. crassus , while in most cases the content of these capsules was degraded to amorphous matter. Occurrence of these objects was correlated with the number of encapsulated larvae in the swimbladder wall. We were able to show, that the cysts contained disintegrated L3 larvae by amplification and subsequent sequencing of large subunit ribosomal rRNA. Furthermore we identified repeated infections with high doses of larvae as prerequisites for the processes of encapsulation in infection experiments.    Conclusion  Under high infective pressure a large percentage of L3 larvae of  A. crassus  coming from the gut lumen are eliminated by the natural host within its intestinal tissue. It is possible to reproduce this condition in infection experiments. We provide a fast, easy and reliable PCR-based method for identification of encapsulated swimbladder parasites.

Massive encapsulation of larval Anguillicoloides crassus in the intestinal wall of Japanese eels