Sorghum is a potential energy crop thanks to its high biomass productivity and low input. Biomass yield in sorghum is defined by height and maturity. To develop molecular breeding tools for genetic improvement of these two traits, we have identified simple sequence repeat markers linked to height and maturity using a pool-based association mapping technique. The sorghum mini core collection was evaluated across five environments for height and maturity. Seven tall and seven short accessions were selected based on their height in all environments. Likewise, six early- and 10 late-maturing accessions were selected mostly based on their maturity in two post-rainy seasons. Two additional height pools were constructed based on phenotypes in one environment. The three pairs of pools were screened with 703 SSR markers and 39 polymorphic markers were confirmed by individual genotyping. Association mapping of the 39 markers with 242 accessions from the mini core collection identified five markers associated with maturity or height. All were clustered on chromosomes 6, 9, and 10 with previously mapped height and maturity markers or QTLs. One marker associated with both height and maturity was 84 kb from recently cloned Ma1. These markers will lay a foundation for identifying additional height and maturity genes in sorghum.