Background Animals are thought to achieve lignocellulose digestion via symbiotic associations with gut microbes; this view leads to significant focus on bacteria and fungi for lignocellulolytic systems. The presence of biomass conversion systems hardwired into animal genomes has not yet been unequivocally demonstrated. Results We perform an exhaustive search for glycoside hydrolase (GH) genes from 21 genomes representing major bilaterian (Ecdysozoa, Spiralia, Echinodermata and Chordata) and basal metazoan (Porifera and Cnidaria) lineages. We also assessed the genome of a unicellular relative of Metazoa, Capsaspora owczarzaki and together with comparative analyses on 126 crustacean transcriptomes, we found that animals are living bioreactors at a microscale as they encode enzymatic suites for biomass decomposition. We identified a total of 16,723 GH homologs (2373 genes from animal genomes and 14,350 genes from crustacean transcriptomes) that are further classified into 60 GH families. Strikingly, through phylogenetic analyses, we observed that animal lignocellulosic enzymes have multiple origins, either inherited vertically over millions of years from a common ancestor or acquired more recently from non-animal organisms. Conclusion We have conducted a systematic and comprehensive survey of GH genes across major animal lineages. The ability of biomass decay appears to be determined by animals’ dietary strategies. Detritivores have genes that accomplish broad enzymatic functions while the number of GH families is reduced in animals that have evolved specialized diets. Animal GH candidates identified in this study will not only facilitate future functional genomics research but also provide an analysis platform to identify enzyme candidates with industrial potential. Electronic supplementary material The online version of this article (10.1186/s12864-018-4861-0) contains supplementary material, which is available to authorized users.