Small RNAs are a diverse category of nuclear-encoded non-coding RNAs that play multiple, central functions in eukaryotic development, stress responses and many other biological processes. The major two types of small RNAs are microRNAs (miRNAs) and silencing RNAs (siRNAs). The major focus of this project is the role of and divergence among sRNAs during cotton diploid divergence, polyploid formation, and cotton domestication. Accordingly, millions of small RNA sequences from next generation sequencing have been generated and analyzed from respective A- and D- diploid cotton and AD1 (upland) wild and domesticated polyploid cotton species. Based on recently published A2 (G.arboreum) and D5 (G. raimondii) genome assemblies, the composition, expression and evolutionary origins of the miRNA families is being characterized.