To study the genetic diversity of the Eurasian coot (Fulica atra), 16 novel microsatellites were isolated and characterised using a (AC)₁₂-enriched genomic library. Polymorphism of each locus was detected in 19 individuals from Weishan Lake and Zhaoyang Lake, both located in Shandong Province, China. These microsatellite loci revealed 3–12 alleles in two populations. One locus (Fa6) showed significant deviations from Hardy–Weinberg equilibrium in the Zhaoyang Lake population. By means of Principal Coordinates Analysis, 19 individuals were divided into two groups, which verified they were from two populations. These novel microsatellites will be useful for further studies and genetic analyses of the Eurasian coot.