The invention discloses a primer composition for identifying the ecotype of indica subspecies of rice and use thereof. The primer composition disclosed by the invention comprises the following primer pairs: a primer pair rm 216 consisting of DNAs represented by sequences 1 and 2, a primer pair rm225 consisting of DNAs represented by sequences 3 and 4, a primer pair rm235 consisting of DNAs represented by sequences 5 and 6, a primer pair rm25 consisting of DNAs represented by sequences 7 and 8, a primer pair rm 23 consisting of DNAs represented by the sequences 9 and 10, a primer pair rm 244 consisting of DNAs represented by sequences 11 and 12, a primer pair rm 253 consisting of DNAs represented by sequences 13 and 14, a primer pair rm 267 consisting of DNAs represented by sequences 15 and 16, a primer pair rm 296 consisting of DNAs represented by sequences 17 and 18, a primer pair rm 223 consisting of DNAs represented by sequences 19 and 20 and a primer pair rm 258 consisting of DNAsrepresented by sequences 21 and 22. The primer composition discloses by the invention can be used for identifying the ecotype of the indica subspecies of rice, has the advantages of quickness, convenience, high efficiency, high sensitivity, high identifying capacity, accurate and reliable result and the like.