Various methods have been used to track seed dispersal of large-seeded species; however, the influence of different seed tracking methods on ecological outcomes of seed dispersal by animals is not well evaluated. Acorn removal by food hoarding animals and the following seedling establishment of Mongolian oak (Quercus mongolica) were investigated in Xiaoxing’anling Mountain, Heilongjiang, northeastern China, by using four different marking methods: plastic tagging, nail insertion, hole drilling, and isotope labeling. The acorn removal speed differed among marking methods, with plastic-tagged acorns being removed more slowly than those marked with nails, holes, and isotope. By checking the attached cotyledons and performing isotope analyses, more seedlings were found to establish from nailed acorns and isotope-soaked acorns than from drilled acorns and plastic-tagged acorns. Plastic-tagged acorns were transported closer than those marked with nails, holes, and isotope. Moreover, seedlings were often found clustered in caches containing acorns marked with plastic tags. Low level of cotyledon predation by animals makes it possible to directly identify focal seedlings of white oaks based on the attached cotyledons. Considering cotyledon predation by animals, coupling minor modification of cotyledons with isotope labeling appears to be an easy way to explore the actual pattern of seed dispersal of large-seeded trees, e.g., oaks.