Cidaroid echinoids (sea urchins) are known to feed on Neocrinus decorus (Baumiller et al., 2008). To escape predation the crinoids break off a section of stem and then use their arms to crawl away quickly from the slow-moving cidaroids.
Blue-headed wrasse (Thalassoma bifasciatum) and dusky damselfish (Stegastes fuscus) have also been shown to predate N. decours in experiments (McClintock et al., 1999). This has been suggested as the reason why stalked crinoids are no longer found on reefs as they have no defence against these predators.
Neocrinus sea lilies are vulnerable to parasites and/or diseases which affect the calcite plates. Infections cause calcite overgrowths of the plates, producing shapes and malformations similar to plant galls.