Long non-coding RNAs (lncRNAs) are RNA molecules with a transcript length of >200 nt which do not encode proteins, however, they have important functions in the form of RNA at transcriptional level, post-transcriptional level, and epigenetics. MALAT-1 is the first discovered lncRNA in non-small cell lung cancer and its orthologs have been found in zebrafish in the recent years. The present study aimed to determine the expression and possible function of MALAT-1 in the embryonic development of zebrafish. The results of qPCR or in situ hybridization showed that MALAT-1 was dynamically expressed in zebrafish embryonic development and it was widely expressed in brain, eye, heart, and muscle of adult fish. By morpholino knockdown of MALAT-1, zebrafish embryos were found to have smaller body curvature, smaller eyes, enlarged pericardium, and reduced pigmentation. In particular, after morpholino knockdown of MALAT-1, the morphologically defective otic capsule was found to be smaller than the control fish. These results suggest that MALAT-1 may play a key role in the embryonic nervous system development of zebrafish. In addition, we also determined the expressions of seven development-related genes (Scyl1, egr1, oc90, vsx1, nkx2.5, vmhc, and gata4) after MALAT-1 knockdown and found that four genes egr1, nkx2.5, gata4, and vmhc were up-regulated, suggesting a potential regulatory role of MALAT-1 on these development-related genes.