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Global declines in biodiversity have stimulated much research into the consequences of species loss for ecosystems and the goods and services they provide. Species at higher trophic levels are at greater risk of human-induced extinction yet remarkably little is known about the effects of consumer species loss across multiple trophic levels in natural complex ecosystems. Previous studies have been criticized for lacking experimental realism and appropriate temporal scale, running for short periods that are not sufficient to detect many of the mechanisms operating in the field.We manipulated the presence of two predator species and two groups of their prey (primary consumers) and measured their independent and interactive effects on primary producers in a natural marine benthic system. The presence of predators and their prey was manipulated in the field for 14 months to distinguish clearly the direct and indirect effects of predators on primary producers and to identify mechanisms driving responses.We found that the loss of either predator species had indirect negative effects on species diversity and total cover of primary producers. These cascading effects of predator species loss were mediated by the presence of intermediate consumers. Moreover, the presence of different intermediate consumers, irrespective of the presence or absence of their predators, determined primary producer assemblage structure. We identified direct negative effects of predators on their prey and several indirect effects of predators on primary producers but not all interactions could have been predicted based on trophic level.Our findings demonstrate the importance of trophic cascade effects coupled with non-trophic interactions when predicting the effects of loss of predator species on primary producers and consequently for ecosystem functioning. There is a pressing need for improved understanding of the effects of loss of consumers, based on realistic scenarios of diversity loss, to test conceptual frameworks linking predator diversity to variation in ecosystem functioning and for the protection of biodiversity, ecosystem functioning and related services.