Myrtaceae species are the most significant family of economic and ecological importance in Australia, but many are threatened by myrtle rust infection caused by Austropuccinia psidii. To investigate the genetic base of resistance in Myrtaceae, we conducted a comprehensive analysis of NBS-LRR gene repertoires using long-read sequences of 27 species. We predicted over 1.0 million protein-coding gene models, out of which 45.8k encode both NBS and LRR domains. We detected 260 unique domains with 5,835 frequency of integration into NBS-LRR, out of which 2605 (43.1%) were accounted by a single Jacalin domain, highly integrated into C-terminal of NBS domain that encodes N-terminal TIR-domain (TNJ). Phylogenetic analysis shows TNJ forms a monophyletic between the TNL clades. Sequence alignment analysis shows all the important nucleotide-binding motifs, and functional amino-acid residues including the catalytic glutamic acid were conserved in TNJ. Shannon entropy and positive selection analysis have determined rapidly evolving TNJ clades with over 80.4% of the detected hyper-variable sites and 76.5% of amino-acid positions that underwent positive selection clustered on the Jacalin region. Our findings reveal that surfaces of Jacalin domain would potentially harbour a cluster of pathogen recognition specificity determining residues in Myrtaceae with Jacalin as a substitute for LRR. The result further show that different plant families could harbour unrecognised diversity of recognition specificity determining domains that have evolved in response to lineage-specific stressors.