Amniotic fluid‐derived mesenchymal stem cells (AF‐MSCs) are autologous to the fetus and represent a potential alternative source for the regenerative medicine and treatment of perinatal disorders. To date, AF‐MSCs differentiation capacity to non‐mesodermal lineages and epigenetic regulation are still poorly characterized. The present study investigated the differentiation potential of AF‐MSCs toward neural‐like cells in comparison to the mesodermal myogenic lineage and assessed epigenetic factors involved in tissue‐specific differentiation. Myogenic and neural differentiation assays were performed by the incubation with specific induction media. Typical MSCs markers were determined by flow cytometry, the expression of lineage‐specific genes, microRNAs and chromatin modifying proteins were examined by RT‐qPCR and Western blot, respectively. AF‐MSCs of normal and fetus‐affected gestations had similar stem cells characteristics and two‐lineage potential, as characterized by cell morphology and the expression of myogenic and neural markers. Two‐lineage differentiation process was associated with the down‐regulation of miR‐17 and miR‐21, the up‐regulation of miR‐34a, miR‐146a and DNMT3a/DNMT3b along with the gradual decrease in the levels of DNMT1, HDAC1, active marks of chromatin (H4hyperAc, H3K9ac, H3K4me3) and the repressive H3K9me3 mark. Differentiation was accompanied by the down‐regulation of PRC1/2 proteins (BMI1/SUZ12, EZH2) and the retention of the repressive H3K27me3 mark. We report that both AF‐MSCs of normal and fetus‐affected gestations possess differentiation capacity toward myogenic and neural lineages through rather similar epigenetic mechanisms that may provide potential applications for further investigation of the molecular basis of prenatal diseases and for the future autologous therapy.