The objective was to test the application of a novel, non-destructive photo-method estimating the larval encystment of one of the highly threatened unionid mussels, the freshwater pearl mussel (Margaritifera margaritifera) on the gills of its host fish, brown trout (Salmo trutta). There were significant correlations between the encystment intensity based on microscope counts and using the new photo-method for both young-of-the-year and older brown trout just after the encystment in October 2007 and just before larval release from the host fish in June 2008. The mean encystment intensity based on the two methods did not differ from each other for the two age classes of trout when based on comparisons including all individuals. An aquaria experiment showed that there were no differences in survival or growth between fish subjected to the treatments: photo-method and individual marking, photo-method and a control. When applied to encystment in single streams, there were significant correlations between the mean encystment intensity in each stream based on the methods for both trout age classes. Therefore, it may be possible to get reliable estimation of the encystment rates without injuring the mussel or the host fish, which may also be used in restoration and cultivation work. Furthermore, the larvae of M. margaritifera are among the smallest of all the worldwide-distributed, threatened unionid mussel species. The photo-method may therefore also be used for other mussel species with larger larvae, as they are more easily recognized on photos. Therefore, it may now be possible to investigate every life stage of unionid species without using harmful methods at all.