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Cold tolerance and the green period are key traits in the breeding of zoysiagrass (Zoysia Willd.). Identifica-tion of molecular markers associated with cold tolerance and the green period of zoysiagrass will contribute to efficient selection of elite cultivars. These two traits were measured in 96 zoysiagrass accessions in 2004 and 2005-2006, respectively. The mapping population was screened with 29 pairs of simple sequence repeat (SSR) primers and 54 pairs of sequence-related amplified polymorphism (SRAP) primers. A multi-loci in silico mapping approach implemented with an empirical Bayes method was applied for association mapping of cold tolerance and green period. We detected 254 SSR polymorphic loci and 338 SRAP polymorphic loci, among which three SSR loci (Xgwml31-3B-187, Xgwm469-6D-194 and Xgwm234-5B-244) and one SRAP locus (MellEm7-406) were significantly associated with cold tolerance with effect values of 57.83%, 38.05%, 36.92% and 37%, respectively. Three SSR loci (Xgwml32-6B-225, Xgwml 11-7D-34 and Xgwml02-2D-97) and two SRAP loci (Mel9Em5-359 and Mel6Em8-483) were significantly associated with the green period with effect values of 79.54%, 62.59%, 99.04%, 49.01% and 82.57%. These markers will be useful for genetic improvement of the cold tolerance and green period of zoysiagrass by marker-assisted breeding. [ABSTRACT FROM AUTHOR]