Objective:To identify small supernumerary marker chromosome by application of multiplex ligation-dependent probe amplification (MLPA)and array comparative genomic hybridization (aCGH). Methods:One case with abnormal mentality was indentified with de novo small supernumerary marker chromosome. G-banding analysis indicated that the patient has a karyotype of 47,XY,+Mar. MLPA was applied to investigate the origin of small supernumerary marker chromosome. Moreover,aCGH was used to define the precise location and size of de novo chromosome. Results:The result of MLPA showed the patient had duplication in 18p11.21 and 18p11.32;aCGH revealed that there was 15 Mb duplication from 18 p11.21-p11.32 in the patient. MLPA and aCGH revealed the presence of small supernumerary marker chromosome,which was derivative from the short arm of chromosome 18. Conclusion:The technologies of MLPA and aCGH can be used for identifying the origin of small supernumerary marker chromosome and defining the loci of the chromosome and can be applied to genetics analysis.