MicroRNAs are a large class of small, non-coding RNAs that post-transcriptionally regulate their target mRNAs through cis-regulatory elements called "microRNA binding sites". Studying the evolution of gene regulation is important for three general reasons. First, regulatory mutations can cause disease; second, understanding how cis-regulatory elements evolve will help us design algorithms for predicting these elements; third, regulatory evolution is important for understanding morphological evolution and speciation. In this talk I will first discuss the evolution of microRNAs and their binding sites over two very different time-scales: between different animal clades and within humans. Then I will discuss recent work on comparing different methods for predicting microRNA binding sites using population genomics data from Drosophila.