MicroRNAs (miRs) are small noncoding RNAs that typically act as regulators of gene expression by base pairing with the 3' UTR of messenger RNAs (mRNAs) and either repressing their translation or initiating degradation. Descriptions of the molecular origins of independent miR molecules currently support the hypothesis that many miR hairpins were generated by the adjacent insertions of two related transposable elements (TEs) at one genomic locus. Thus transcription across such TE interfaces establishes many, if not the majority of functional miRs. We have recently completed an in depth analysis of the genomic origins of annotated miR loci, detailing the formations of 3,605 distinct miR loci primarily from TEs. Interestingly, our analyses also identify evidence for a second, novel mechanism of miR locus generation through describing the formation of 273 miR loci from mutations to other forms of noncoding RNAs. The implications of these findings are substantial for understanding how (in particular) TEs confer increased genomic fitness, describing miR transcriptional regulations, and making accurate miR target predictions. As such, hypothesizing that a miR and its mRNA target sites might actually be formed in parallel by the ongoing colonization of a common ancestral transposable element, led us to develop a novel miR target prediction strategy in which we limit miR target searches to mRNAs containing the TE (or noncoding RNA) initially giving rise to a miR: OrbId (Origin-based Identification of microRNA targets). In stark contrast to the principal miR target algorithms (which rely heavily on target site conservation across species and are therefore most effective at predicting targets for older miRs), we find OrbId is particularly efficacious at predicting the mRNA targets of miRs formed more recently in evolutionary time.