Seed hoarding animals may distinctly impact individual fitness of plants as well as plant community dynamics in terms of differential seed consumption and seed dispersal. Addressing methodological challenges and constraints in understanding the role of seed dispersal mutualisms, we tested different seed tagging methods for relatively small seeds. We selected two study areas with dense ground vegetation, irregular terrain, and seed predator guilds with comparatively high dispersal and seed removal potential. We tested three different tagging methods, offering untagged and tagged seeds on experimental dishes: (1) wire threads with plastic flags fixed with solvent-free glue, (2) wire threads with plastic flags twisted around a beechnut, (3) and radio-transmitters fixed with solvent-free glue. Seed predators did not show any preferences for tagged or untagged seeds or for a certain tagging method at any point of time. Instead, both tagged seeds and untagged control seeds were removed from the dishes to a high degree (up to 100%) after 25-35 days. In both study areas, seeds with radio-transmitters experienced longer transport distances with a maximum of nearly 60 m and distances also differed between study areas. In one study area, higher portions of radio-tagged seeds could be recovered than for the flag-tagged seeds. Significantly more seeds tagged with radio-transmitters were cached than expected. Given the advantages and limitations of each approach, a combination of flag-tagging and radiotelemetry (not on the same seed) may be the best solution for tracking seed fate in dense vegetation or irregular terrain.