The mechanisms underlying antigen receptor germline gene diversification have always been a topic of intensive study. Here, we discovered that the frequency of stem-loop sequences in the antigen receptor germline gene region is remarkably higher than the genomic background. By analyzing these stem-loop sequences' similarity and distribution patterns, we found that clustered regularly interspaced homologous stem-loop pairs (CRIHSP) are widely present on the germline genes of antigen receptors in different species. By examining genomic stability under activation-induced cytidine deaminase (AID) overexpression, we found that CRIHSP sequences are preferred targets for AID. In addition to influencing the functions of AID and recombination-activating gene (RAG) 1/2 proteins, our findings indicate that CRIHSP also stabilize regions with high levels of homologous sequences and promote homologous recombination. Additionally, we observed that most recombination signal sequences (RSSs) form CRIHSP-like sequences with adjacent stem-loops, which influences RSS-mediated gene recombination under the action of RAG1/2 proteins. We speculate that CRIHSP are very likely to play an important role in orchestrating the generation of antigen receptor diversity, such as affecting somatic hypermutation (SHM) and antigen receptor germline gene rearrangement, and genomic stability within antigen receptor germline genes. However, detailed studies are required to delineate the underlying molecular mechanisms.