30 MicroRNAs (miRNAs) are endogenous small noncoding RNAs that post 31 transcriptionally regulate gene expression and are involved in many biological 32 processes including host-pathogen interactions. However, the potential role of 33 miRNAs in the responses of eastern honeybees to Nosema ceranae invasion is 34 completely unknown. Here, the expression profiles and differentially expressed 35 miRNAs (DEmiRNAs) in the midguts of Apis cerana cerana workers 7 and 10 days 36 post infection (dpi) with N. ceranae were investigated via small RNA sequencing and 37 bioinformatics. In total, 529 miRNAs highly conserved between various species and 38 25 novel miRNAs with varied expressions were identified for the first time. In 39 addition, stem-loop RT-PCR confirmed the expression of 16 predicted miRNAs, 40 validating their existence. Eight up-regulated miRNAs and six down-regulated 41 miRNAs were detected in midguts at 7 dpi, while nine and three miRNAs were 42 significantly up-regulated and down-regulated, respectively, in midguts at 10 dpi. In 43 addition, Venn analysis showed that five DEmiRNAs were shared, while nine and 44 seven DEmiRNAs were specifically expressed in midguts at 7 and 10 dpi, 45 respectively. Gene ontology analysis suggested that a portion of the DEmiRNAs and 46 corresponding target genes were involved in various biological processes, cellular 47 components, and molecular functions including immune system processes and 48 response to stimulus and signaling. Moreover, KEGG pathway analysis shed light on 49 the potential functions of some DEmiRNAs in the regulation of target genes engaged 50 in material and energy metabolism, cellular immunity such as endocytosis and 51 phagosome, and the humoral immune system, including the Jak-STAT and MAPK 52 signaling pathways. Further investigation demonstrated a complex regulation network 53 between DEmiRNAs and their target mRNAs, with miR-598-y, miR-252-y, miR-92-x 54 and miR-3654-y at the center of the network, implying their key parts in host 55 responses. This comprehensive miRNA transcriptome analysis demonstrated that N. 56 ceranae invasion influenced the expression of miRNAs in the midguts of A. c. 57 ceranae workers; the results can not only facilitate future exploration of the regulatory 58 roles and mechanisms of miRNAs in hosts' responses, especially their immune 59 3 responses to N. ceranae, but also provide potential candidates for further investigation 60 of the molecular mechanisms underlying eastern honeybee-microsporidian 61 interactions. 62