Increasing evidence suggests that non-coding RNAs have multiple important roles in transcriptional regulation, and also contribute to the expansion of genome complexity. Here, we attempted to perform an integrative analysis of miRNA-lncRNA in mammals to reveal their potential evolutionary relationships in transcriptional regulation network. The lncRNA of H19 gene includes an internal small non-coding RNA, miR-675. The H19 gene was conserved as well as the neighbor Igf2 coding gene and internal miR-675 gene, although they were involved in various location distributions and phylogenetic relationships. Both miR-675-5p/3p have been reported as potential negative regulatory molecules, but the canonical miRNA was more conserved than the passenger strand. These results implicated that the imprinted coding and non-coding gene cluster indicated similar evolutionary patterns. The lncRNA and internal miRNAs may have versatile roles in multiple biological processes, including in tumorigenesis as potential ncRNA regulatory molecules. The phylogenetical conservation of the imprinted cluster may be also derived from the functional implications and evolutionary pressures. The study will enrich the study of potential crosstalk of miRNA-lncRNA and mRNA-ncRNA.