Control of organ growth by coordinating cell proliferation and differentiation is a fundamental developmental process. In plants, postembryonic root growth is sustained by the root meristem. For maintenance of root meristem size, the rate of cell differentiation must equal the rate of cell division. Cytokinin and auxin interact to affect the cell proliferation and differentiation balance and thus control root meristem size. However, the genetic and molecular mechanisms that detemine root meristem size still remain largely unknown. Here we report that dar2 mutants produce small root meristems due to decreased cell division and early cell differentiation in the root meristem. dar2 mutants also exhibit reduced stem cell niche activity in the root meristem. DAR2 encodes a LIM domain-containing protein and shows an expression peak in the border between the transition zone and the elongation zone. Genetic analyses show that DAR2 functions downstream of cytokinin and SHORT HYPOCOTYL2 (SHY2/IAA3) to maintain normal auxin distribution by influencing auxin transport. Further results indicate that DAR2 acts through the PLETHORA (PLT1/2) pathway to influence root stem cell niche activity and therefore control root meristem size. Collectively, our findings identify the role of DAR2 in root meristem size control and provide a novel link between several key regulators influencing root meristem size.