Microsatellites were identified and characterised for a worldwide invasive weed, Ageratina adenophora, based on the Illumina sequencing technology. Using the assembled genomic sequences obtained from the Illumina GAII sequencing platform, a total of 3012 microsatellites were identified, of which mono-, di-, tri-, tetra-, penta-, and hexa-nucleotide repeats were 181 (6.0%), 1379 (45.8%), 1064 (35.3%), 220 (7.3%), 73 (2.4%) and 95 (3.2%) respectively. The AC/GT and GAT/ATC motifs were the most frequent motif types of di-nucleotide and tri-nucleotide repeats respectively. To validate the newly identified simple sequence repeat markers, 15 primer pairs were randomly selected to test in 24 individuals of A. adenophora, and all of these primer sets could amplify PCR products of expected size. Of them, eight loci displayed polymorphism with the number of alleles per locus ranging from two to four and values for observed and expected heterozygosities ranging from 0.042 to 1 and from 0.082 to 0.551, with the averages of 0.578 and 0.371 respectively. These novel microsatellites should be useful for investigation of the genetic structure and genetic diversity between the invasive and native populations of this species.