Seed maturation and its accompanying seed reserve production are accomplished through concerted activity of many gene products and biological pathways. To delineate their underlying transcriptional gene regulatory networks we examined transcriptomes of cotyledon at six distinct seed maturation stages, and further inferred 305 transcription factor regulatory networks through integrating them with additional 115 transcriptomes of various soybean seed related tissues. In addition, we sequenced 292 million small RNAs of 18 small RNA libraries from identical tissues, and identified 129 novel cotyledon microRNAs. Fifty-four miRNAs were differentially regulated at their accumulation levels with statistical significance over the course of seed maturation. A rich presence of intronic miRNAs and a high miRNA gain/loss rate were observed in cotyledon. Expression patterns of the cotyledon miRNAs and their predicted target transcripts were compared to predict their functional miRNA-target mRNA interactions based on negative correlation of their expression patterns. The topology of the cotyledon miRNAs in the transcription factor gene networks was determined; and biological pathways that are potentially regulated by the transcription factor networks were determined. Detailed results will be presented and discussed. The research is supported by USDA/ARS and the United Soybean Board.