To determine genetic differentiation of rice (Oryza sativa L.) across a latitudinal gradient, a total of 386 rice varieties, five African rice varieties, and 52 wild rice accessions mainly from a wide range of Asia were analyzed using insertion and deletion (InDel) molecular markers. Principal component analysis divided rice into two distinct groups, although African rice and wild rice did not show such grouping. Results indicated significant indica–japonica differentiation of rice adapted to a wide range of environments, contrasting with African rice and wild rice. Analysis of the geographic distribution indicated a clear pattern for different types of rice, in which indica varieties were found across a wide range of latitudes from ∼2° S to 40° N and japonica mostly limited to latitudes greater than 15° N. Most intermediate types were distributed in regions at latitudes lower than 27° N. Correlation between rice types and temperature along the latitude gradients suggested that indica varieties are less sensitive to temperature along the latitude ranges but japonica varieties are highly sensitive to temperature. The distribution and differentiation of various types of rice across the large latitudinal range is most likely the consequence of their adaptation to ecological and environmental factors, especially temperature. This, together with the accurate determination of indica and japonica types has important implications for hybrid rice breeding through selecting properly differentiated parents.