Automated separation and classification of touching or overlapping chromosomes in a metaphase image is a critical step in computer-aided chromosome analysis. The advent of the multiplex fluorescence in situ hybridization (M-FISH) technology enables multi-spectral chromosome image with rich spectral information and DAPI image with abundant texture information. This paper presents a fusion classification scheme to improve the segmentation of overlapping and touching chromosomes. First, the texture and spectral information is fused to partition the chromosome cluster into a series of homologous regions. Then a graph-theoretical classification and pairing method is proposed to resolve any remaining ambiguity of the aforementioned separation process. Experiment results demonstrate that the proposed method outperforms conventional multi-spectral classification methods in touching and overlapping chromosome separation.