One of the most complex cell transformations in biology is the remodeling of a fertilized oocyte into a totipotent zygote. There is no transcription during this event, and therefore mRNAs and proteins accumulated in the oocyte during oogenesis are utilized until zygotic genome activation. In order to differentiate into somatic cells, the embryo must erase the totipotency signature coming from the oocyte cytoplasm in the somatic blastomeres. In this study, the microRNAome profiles of oocytes and early embryos before and after zygotic genome activation were identified. By using next-generation high-throughput pyrosequencing and miRNA microarray techniques, miRNAome profiles of Caenorhabditis elegans oocytes (mitotic and meiotic) and early embryos before (2-blastomere stage) and after (8-blastomere stage) zygotic genome activation were generated. Besides observing results similar to those of previous reports, new miRNAs were identified whose expression levels changed during this transformation. After selection and polymerase chain reaction validation of the candidate miRNAs, downstream targets were identified by using bioinformatic tools and they were subjected to pathway analysis. Further analysis of the identified miRNAs in this study may provide a better understanding of the regulation of early embryonic development, germline-soma differentiation, oocyte-embryo transition, and maintenance of totipotency status.