Black rice is considered as a functional food for its high anthocyanin content, expressed as purple-black grain rice color. The study was aimed to determine the correlation between total anthocyanin content with L*, a*, and b* color variables, total anthocyanin content with color morphology and total anthocyanin content with microsatellite markers. Eleven local black rice varieties derived from the Yogyakarta Assesment Institute of Agriculture Technology collections and two varieties of white rice (Situbagendit and Inpari 6 Jete) were planted on plastic pots in green house. The trial was arranged in a completely randomized design with five replications. At three weeks after planting, leaf samples were taken for DNA isolation and further PCR amplifications using four microsatellite markers (RM 180, RM 220, RM 224 and RM 252). The black rice grains were observed based on color morphology using a chromameter and analyzed for their anthocyanin content. Regression, correlation, and path analyses were conducted to determine the relationship between total anthocyanin content and L* a* b * color variable, color morphology, and microsatellite markers. Results showed that there were correlation between total anthocyanin content and color variables (rL* = -0.568, ra* = -0.561, rb*= 0.844). The total anthocyanin content were also correlated with color scores of morphology and total microsatellite markers (rRM 180 =-0.419, rRM 220 =0.27, rRM 224 =-0.493, rRM 252 =0.265) and color scores of morphology, r = -0.442. Selection of high-anthocyanin content on rice could use the color variable criteria (L* and a* low, and b* high). Microsatellite markers RM 220 and RM 252 can be used as molecullar markers for identification of rice having high anthocyanin content.