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Invertebrates do not possess adaptive immunity but have evolved a variety of unique repertoires of innate immune sensors. In this study, we explored the immune diversity and specificity of invertebrates based on the lophotrochozoan <i>RLRs</i>, a major component in antiviral immune recognition. By annotating <i>RLRs</i> in the genomes of 58 representative species across metazoan evolution, we explored the gene expansion of <i>RLRs</i> in Lophotrochozoa. Of note, the N-terminal domains of lophotrochozoan <i>RLRs</i> showed the most striking diversity which evolved independently by domain grafting. Exon–intron structures were revealed to be prevalent in the domain grafting of lophotrochozoan <i>RLRs</i> based on an analysis of sibling paralogs and orthologs. In more than half of the cases, the mechanism of ‘exonization/pseudoexonization’ led to the generation of non-canonical N-terminal domains. Transcriptomic studies revealed that many non-canonical <i>RLRs</i> display immune-related expression patterns. Two of these <i>RLRs</i> showed obvious evidence of positive selection, which may be the result of host defense selection pressure. Overall, our study suggests that the complex and unique domain arrangement of lophotrochozoan <i>RLRs</i> might result from domain grafting, exon–intron divergence, expression diversification, and positive selection, which may have led to functionally distinct lophotrochozoan <i>RLRs</i>.