Y-box-binding protein 1 (Ybx1, YB-1), also known as Y-box transcription factor, is involved in a variety of biological processes and pathways, including embryogenesis, reproduction and development in vertebrates. Several non-coding RNAs regulate Ybx1 signaling. However, the role of long non-coding RNAs (lncRNAs) in embryogenesis remains incompletely understood. Here, we investigated the possible involvement of lncRNAs in Ybx1-mediated regulation of vertebrate development by performing systematic transcriptome analysis of RNA sequencing data derived from ybx1 homozygous mutant zebrafish on day5 (day5_ybx1 ) and wild type zebrafish on day5 and day6 (day5_ybx1 , day6_ybx1 ). We identified several lncRNAs affected by ybx1 disruption that may target redox-related genes such as duox and noxo1a. Knockdown of three selected lncRNAs led to morphological deformation of larvae, implying an involvement of these lncRNAs in zebrafish embryo development. In summary, our study provides new insights into the lncRNA-mediated mechanisms underlying development in Ybx1 deficient zebrafish larvae.