DeAnnIso, is an online tool, that is designed for Detection and Annotation of IsomiR from small RNA sequencing data. DeAnnIsomiR can detect isomiR of each subject based on the methodology, we have described in our previously published pipeline CPSS. The detected isomiRs will be classified into different categories (e.g. add, trim, internal modification). The isomiRs will be aligned with canonical miRNA, and will be annotated with expression, constitution, SNP, and an in-house dataset (contains 308,919 isomiRs detected from 2,727 samples). It can also extract differentially expressing isomiR between two samples. In addition, IsomiR Bank provides targets prediction and enrichment analysis to evaluate the effects of isomiRs on target selection. Currently, DeAnnIso can analyze data from eight species (Arabidopsis thaliana, Drosophila melanogaster, Danio rerio, Homo sapiens, Mus musculus, Oryza sativa, Solanum lycopersicum and Zea mays).