Geographically, different rice ecosystems are found throughout the various regions of Thailand and since ancient times, traditional upland and lowland rice cultivars from these regions have played a key role in both production as a staple food and rice germplasm for variety improvement. In this study, a polymorphism of chloroplast DNA and the physiological marker of 74 upland and lowland rice accessions were collected and examined from all regions of the country. Based on the results of the phenol reaction, the hulls of all upland rice cultivars from the northern region of Thailand, but not those from the northeastern region, showed unchanged color of the hulls when soaked in a 1.5% phenol solution and were scored as positive (Ph^-). Lowland rice cultivars from other regions in Thailand turned to black of hull color (Ph ⁺). Upland rice from the Northern and northeastern regions carried Non-Deletion (ND) type ORF100, but only a few lowland rice samples from the central region carried the ND type. Most of the lowland rice cultivars showed deletion type (D type) of the region. Six plastid subtype ID sequences (6C7A, 7C7A, 7C6A, 8C8A, 9C7A and 9C8A) were found in the collected samples. Upland rice from both the northern and northeastern regions carried three (6C7A, 7C7A and 7C6A) PS-ID sequences. The subtype 8C8A was not found in the northern region samples, but predominated in the northeastern samples. The PS-ID sequences of upland (6C7A and 7C6A) and lowland (8C8A) black rice cultivars were different, suggesting that this molecular marker is useful in terms of DNA marker-assisted selection for black rice variety improvement.