Depending on the purpose of rice production and rice field conditions, the genotypic traits will be selected in different ways. For the aim of identifying candidate genes associated with photoperiod insensitivity (PHISE), the whole genome sequence of 20 accessions was analyzed to get Indel information on two photoperiod-sensitivity groups. Within 20 accessions, 2,240 Indels were identified with the definite difference between two photoperiod-sensitivity groups. Almost 2,240 Indels were in chromosome 01. 332 out of 615 indels coding genes were found for rice accessions from 3K and MDI’s rice. Those indels made MDI’s improved rice into ind1b subpopulation and MDI’s landrace to ind3 subpopulation. Interestingly, 332 indels can make eight subpopulations from 3K into one structure as follow: Jap, Subtrop, Trop, Temp, Aus, and Aro subpopulation. Notably, 21 indels were found for classifying the difference between indica improved rice and landrace subpopulation (chromosome 01: 15 indels, chromosome 06: 6 indels) based on the Chi-square analysis method. Twenty-one indels were found in 17 distinct genes for two MDI’s rice groups and ind1b and ind3 from the 3K database.