Objective To investigate the prenatal diagnosis and phenotypic assessment strategies for fetal supernumerary marker chromosomes and derivative chromosomes. Methods Five cases of fetal supernumerary marker chromosomes and one case of fetal derivative chromosomes were diagnosed in the First Affiliated Hospital of Sun Yat-Sen University from March 12, 2010 to November 9, 2012 by conventional chromosome banding, fluorescence in situ hybridization （FISH） and spectral karyotyping （SKY）. These cases were retrospectively reviewed. Combined with the results of ultrasonography, abnormal phenotypes and pregnancy outcomes were evaluated in these cases. Results All of the five supernumerary marker chromosomes were de novo, in which two were mosaic and the remaining three cases were non-mosaic. Of these five cases, two were type 47, XX＋mar and ultrasound indicated abnormal phenotypes. FISH and SKY confirmed that they were＆amp;nbsp;derived from chromosome 4 and 22, respectively. The other three cases were marker chromosome with Turner syndrome karyotype （abnormal phenotypes were not found by ultrasound）, in which two cases were derived from chromosome Y （by FISH） and one case was identified as ring chromosome X （by FISH and SKY）. One de novo derivative chromosome was verified as a product of reciprocal translocation between chromosome 2 and 6 （by FISH and SKY）. Induced abortion was performed in all cases between 25 and 32 gestational weeks. Conclusions By combining conventional chromosome banding, FISH and SKY, the origin and content of supernumerary marker chromosomes and derivative chromosomes can be identified. On this basis, clinical phenotype evaluation and genetic counseling may be offered with the ultrasonographic result.