Endogenous microRNAs (miRNAs) modulate gene expression at the post-transcription level. In plants, a vast majority of MIR genes are thought to be transcribed by RNA Polymerase II (Pol II). However, promoter organization is currently unknown for most plant MIR genes. This deficiency prevents a comprehensive understanding of miRNA-mediated gene networks. In this study, we performed Pol II chromatin immunoprecipitation (ChIP) analysis in Arabidopsis using a genome tiling microarray. Distinct Pol II binding was found at most MIR loci, which allowed prediction of the transcription start sites (TSSs) for 167 MIR genes in Arabidopsis that was validated by average free energy profiling. By employing 99 position weight matrices (PWM), we systematically scanned the regulatory regions upstream of the TSSs. We discovered eleven and ten cis-elements that are statistically over- and under-represented in MIR promoters, respectively. Thus, analysis of Pol II binding provides a new perspective for studying miRNAs in plants.