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Echinococcosis are considered to be potentially lethal zoonotic diseases that cause serious damage to hosts. The metacestode of <i>Echinococcus </i><i>multilocularis</i><i> </i>and <i>E. </i><i>granulosus</i> can result in causing the alveolar and cystic echinococcoses, respectively. Recent studies have shown that non-coding RNAs are widely expressed in <i>Echinococcus </i>spp. and hosts. In this review, the two main types of non-coding RNAs&#8212;long non-coding RNAs (lncRNAs) and microRNAs (miRNAs)&#8212;and the wide-scale involvement of these molecules in these parasites and their hosts were discussed. The expression pattern of miRNAs in <i>Echinococcus </i>spp. is species- and developmental stage-specific. Furthermore, common miRNAs were detected in three <i>Echinococcus</i> spp. and their intermediate hosts. Here, we primarily focus on recent insights from transcriptome studies, the expression patterns of miRNAs and lncRNAs, and miRNA-related databases and techniques that are used to investigate miRNAs in <i>Echinococcus </i>and echinococcosis. This review provides new avenues for screening therapeutic and diagnostic markers.