Following the increase in available sequenced genomes, tissue-specific transcriptomes are being determined for a rapidly growing number of highly diverse species. Traditionally, only the transcriptomes of related species with equivalent tissues have been compared. Such an analysis is much more challenging over larger evolutionary distances when complementary tissues cannot readily be defined. Here, we present a method for the cross-species mapping of tissue-specific and developmental gene expression patterns across a wide range of animals, including many non-model species. Our approach maps gene expression patterns between species without requiring the definition of homologous tissues. With the help of this mapping, gene expression patterns can be compared even across distantly related species. In our survey of 36 datasets across 27 species, we detected conserved expression programs on all taxonomic levels, both within animals and between the animals and their closest unicellular relatives, the choanoflagellates. We found that the rate of change in tissue expression patterns is a property of gene families. Our findings open new avenues of study for the comparison and transfer of knowledge between different species.