The origin of placentation in mammals required a symphony of events from protein innovation to the evolution of regulatory networks that could support successful pregnancy from implantation to full gestation. There is variation across mammals in terms of the types of implantation, degree of invasiveness of the trophoblast into the maternal endometrium, and the type of placenta formed. However, there are some signalling networks, e.g. progesterone receptor signalling, that are shared across the clade. We wished to determine what regulates the diverse molecular interactions and morphologies that underpin successful pregnancy in eutheria. Whilst the relationship between miRNAs and pathophysiology of placenta is well established, their role in early implantation and diversity of implantation strategies is not well understood. We identify a cohort of miRNAs that arose coincident with the emergence of placental mammals (mir-127, -185, -188, -28, -324, -331, -340, -378, -423, -433, -505, -542, and -671). We identify 115 genes under positive selection on the stem eutherian lineage and 88 of these are predicted to be regulated by the 13 stem lineage miRNAs. Using two species of mammal that demonstrate the extremes of implantation strategies (invasive and superficial in humans and bovine respectively), we assessed the response of the endometrial epithelium in terms of expression of these miRNAs to early pregnancy molecules. We show that the 13 stem lineage miRNAs are regulated in a species-specific manner. We propose these species-specific regulatory networks contribute to the diversity of pregnancy morphologies observed in eutheria.