Somatic embryogenesis involves complex molecular signaling pathways. Deregulation of these signaling pathways can transform the emblyogenic callus to non-embryogenic callus. To investigate the miRNA regulation underlying this detrimental transformation in Japanese Larch (Larix leptolepis), we compared miRNA expression profiles between embryogenic and non-embryogenic callus at day 3 and day 14 after sub-culture. Four miRNA families dominated the 165 differentially expressed miRNAs between embryogenic and non-embryogenic callus. Of the four, miR171 was up-regulated, and miR159, miR169, and miR172 were down-regulated in the embryogenic callus. These four families are all abiotic stress-induced miRNAs, and all target transcription factors that regulate a group of genes important for cell differentiation and development, including scarecrow-like (SCL) transcription factor (miR171), apetala2 (miR172), MYB transcription factors (miR159), and NF-YA transcription factor (miR169). Three down-regulated miRNA families in the embryogenic callus are also regulated by ABA, which further shed light into the potential mechanisms underlying the transformation of the embryogenic competence in L. leptolepis. This study represents the first report on the miRNA regulation of the embryogenic and non-embryogenic callus in plant, and thus these four miRNA families provide important clues for further functional investigation. (C) 2010 Elsevier Inc. All rights reserved.