Leaf rust disease caused by Puccinia triticina L. is the most common and prevalent in almost all regions where wheat (Triticum aestivum L.) is grown. A long list of genes providing resistance against leaf rust is there but still a lot need to be deciphered to understand the complete picture of disease resistance. Availability of whole genome sequencing data in public databases has accelerated the molecular biologist efforts to identify and annotate new genes. Cyclophilins (CYPs) are a group of highly conserved proteins and have been found to be crucial in pathogenesis in different plants. With our best knowledge the role of CYP gene against leaf rust disease have not studied in wheat. Therefore, authors conducted a genome wide identification of wheat CYP genes (TaCYPs), their interaction, and change in expression profile during leaf rust infection, and investigation of miRNA-SSRs from CYP genes for their future use in molecular breeding. Biological survey of CYP genes in wheat on genome-wide scale was conducted using amino acid sequences of two A. thaliana CYP genes; AtCYP18-3 and AtCYP19-1 resulted identification of 81 TaCYPs (carried a conserved CLD domain) across all 21 wheat chromosomes. Different physiochemical, subcellular localisation were revealed to the unblocking of the information related to the identified genes. Highly variable gene structure of TaCYPs with a range of 0-14 number of exon/intron with distribution of 15 conserved motifs were annotated. Evolutionary study clustered 81 TaCYPs into three groups GI, GII, and GIII possessing TLP-40 domain, ABH domain, and ring U-Box domain respectively. Searching of potential of gene-specific SSRs lead to the identification of 145 SSR motifs with a range from 1-10 motif repeats and network of miRNAs targeting TaCYPs demonstrated the multiplicity behaviour of miRNAs in a significant manner. Expression analysis was conducted using qRT-PCR on two wheat lines (TR; resistant and CS; susceptible) at two-time point (24 hrs, and 72 hrs after inoculation) for selected TaCYP genes. Expression profiling revealed that out of 25 primers used, four TaCYP genes (XTaCYP-3, XTaCYP-20, XTaCYP-22, and XTaCYP-23) had a distinct expression in two contrasting lines; CS (downregulation) and TR (upregulation). Among all the genes, XTaCYP-8 had maximum upregulation in resistant line with comparison to susceptible line. However, further study need to be conducted to confirm the role of TaCYP-8 against leaf rust resistance. Protein-protein interaction information validated role of CYPs against different stresses. 3D modelled structure of 15 representative TaCYPs were obtained with a maximum 100% similarity. Calculated values of Ramachandran plot evidenced in support of high quality of identified proteins. Therefore, current study identified novel role of CYP genes/markers against leaf rust disease in wheat that can be used in future wheat breeding programs.