Phytocytokines, a class of small secreted peptides (SSPs) with signaling roles, are essential for various plant physiological processes. However, accurately detecting and annotating them remains challenging due to their varied sequence conservation across species and the limited understanding of their biological functions. In apple, the availability of a high-quality genome enabled the exploration of five phytocytokine gene families, selected on the basis of their deregulated profiles in response to biotic stresses: phytosulfokine (PSK), inflorescence deficient in abscission/-like (IDA/IDL), PAMP-induced secreted peptide (PIP), plant peptide containing sulfated tyrosine (PSY), and C-terminally encoded peptide (CEP). Using a custom bioinformatics protocol that combined genome mining, homology searches, peptide motif detection, and chromosomal organization analysis, we exhaustively identified the secreted peptide precursors and associated genes for those five peptide families in apple. Further transcriptomic analyses revealed their deregulation in response to Erwinia amylovora, the causal agent of fire blight in pomoids, and a chemical elicitor (acibenzolar-S-methyl). Additionally, we investigated orthology relationships with Arabidopsis thaliana homologs. Those results represent the first step towards the identification and characterization of apple tree SSPs involved in biotic stress responses.