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<div>Efficient management of wheat rust diseases is challenging since <i>Puccinia</i> spp. can rapidly alter their effector repertoires in response to recognition by resistance genes. Although many putative effectors have been predicted, functional studies have been limited due to the lack of a suitable effector delivery system for wheat. Here we identified two <i>Pseudomonas </i>strains for delivering rust effectors. Twenty effector proteins from <i>P. graminis </i>and <i>P. stiriiformis</i> were screened and nine effectors capable of suppressing host defense responses were identified. Further, we analyzed the small RNA profiles of two wheat cultivars differentially susceptible to <i>P. striiformis</i> to understand changes in gene regulation following infection. A total of 163 novel miRNAs and 182 known miRNAs were identified using 12 small RNA libraries from two cultivars - Louise and Penawawa infected with <i>P. striiformis</i>. 145 miRNAs targeted wheat genes, while 69 miRNAs targeted fungal genes. Of these miRNAs, 53 were differentially expressed (<i>P</i> < 0.05) between the two infected cultivars that varied in their response to rust disease. The majority of fungal targets coded for small, secreted proteins, providing preliminary evidence for cross-kingdom control of gene regulation. Overall, this study contributes to the current repository of wheat effectors and miRNAs; and provides novel information on the yet to be characterized roles for proteins and microRNAs in the wheat-rust interactions.</div>