Alternative splicing is a process producing multiple mRNA isoforms from a single pre-mRNA. In the past, AS was thought to be less frequent in plants than in animals, it is now known to be widespread in plants, thanks for the advance in computational methods and lab techniques. In this talk, I will briefly review methods to identify AS events, including EST-EST comparison, EST-Genome alignment and cross-species EST-Genome alignment. Two computer programs, ASpipe and PASA, are now widely used to identify and annotate transcript isoforms. Several multiple-species studies revealed distinct features in splicing mechanism between plants and animals. Next generation sequences bring great opportunities as well as challenges to AS studies.