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Conservation has long focused on preserving or restoring pristine ecosystems. However, understanding and managing novel ecosystems has grown in importance as they outnumber pristine ecosystems worldwide. While non-native species may be neutral or detrimental in pristine ecosystems, it is possible that even notorious invaders could play beneficial or mixed roles in novel ecosystems. We examined the effects of two long-established non-native species—Philippine deer (Rusa marianna) and feral pigs (Sus scrofa)—in Guam, Micronesia, where native vertebrate frugivores are functionally absent leaving forests devoid of seed dispersers. We compared the roles of deer and pigs on seedling survival, seed dispersal and plant community structure in limestone karst forests. Deer, even at low abundances, had pronounced negative impacts on forest communities by decreasing seedling and vine abundance. By contrast, pigs showed no such relationship. Also, many viable seeds were found in pig scats, whereas few were found in deer scats, suggesting that pigs, but not deer, provide an ecosystem function—seed dispersal—that has been lost from Guam. Our study presents a discrepancy between the roles of two non-native species that are traditionally managed as a single entity, suggesting that ecological function, rather than identity as a non-native, may be more important to consider in managing novel systems.