One of the most fundamental events in plant ontogeny is the specification of the shoot and root apical meristem (SAM and RAM) in embryogenesis. In Arabidopsis, the restricted expression of class III homeodomain leucine zipper (HD-ZIP III) transcription factors (TFs) at the central–apical domain of early embryos is required for the correct specification of the SAM and RAM. Because the expression of HD-ZIP III TFs is suppressed by microRNA165/166 (miR165/6), elucidation of the sites of miR165/6 production and their activity range is a key to understanding the molecular basis of SAM and RAM specification in embryogenesis. Here, we present a comprehensive reporter analysis of all nine Arabidopsis MICRORNA165/166 (MIR165/6) genes during embryogenesis. We show that five MIR165/6 genes are transcribed in a largely conserved pattern in embryos, with their expression being preferentially focused at the basal–peripheral region of embryos. Our analysis also indicated that MIR165/6 transcription does not depend on SCARECROW (SCR) function in early embryos, in contrast to its requirement in post-embryonic roots. Furthermore, by observing the expression pattern of the miR-resistant PHBmu-GFP (green fluorescent protein) reporter, in either the presence or absence of the MIR165Amu transgene, which targets PHBmu-GFP, we obtained data that indicate a non-cell-autonomous function for miR165 in early embryos. These results suggest that miR165, and possibly miR166 as well, has the capacity to act as a positional cue from the basal–peripheral region of early embryos, and remotely controls SAM and RAM specification with their non-cell-autonomous function.