Hop (Humulus lupulus L.) is a dioecious member of the Cannabaceae family, originating in China. Only the female plant is important economically. Our analyses focused on viroids, as important hop pathogens. Hop plant can be infected with four different viroids: hop latent viroid (HLVd), hop stunt viroid (HSVd), apple fruit crinkle viroid (AFCVd) and citrus bark cracking viroid (CBCVd). We focused on the interaction between viroid and plant using two viroids - one that causes mild symptoms (HLVd) and another that causes very serious and strongly expressed symptoms. To analyse the interaction between vd-sRNA and hop transcription, we first assembled the hop transcriptome and in-silico predicted all possible vd-sRNAs (21, 22 and 24 bp) of CBCVd and HLVd. Two tools were used to find hypothetical targets - psRNATarget and UEA sRNA Workbench. We focused our further work on potential targets belonging to one of the following categories 1) targets participate in the metabolism of plant hormones, 2) targets participate in small RNA biogenesis, 3) CBCVd targets of vd-sRNAs from extremely well covered regions of the viroid and 4) Genes with high homology with vd-sRNAs. Changes of target expression were monitored by reverse transcription coupled with quantitative PCR (RT-qPCR). The selected targets showed changed patterns of expression in various tissues of the hops. We found evidence of possible reduced expression for LOX and GATA transcripts. The results obtained in this study will consolidate new research pathways in strategies to combat viroid diseases of hops, as well as other plants.