Ecological immunology is a rapidly expanding field that examines the causes and consequences of variation in immune function in the context of evolution and of ecology. Millions of invertebrate species rely solely on innate immunity, compared with only 45,000 vertebrate species that rely additionally on an acquired immune system. Despite this difference in diversity, most studies of ecological immunology focus on vertebrates. Here we review recent progress derived largely from the mechanistic analysis of invertebrate innate immunity. Using this empirical base, we pose general questions in areas that are of central importance for the development of ecological immunology.