A common task in cytogenetic tests is the classification of human chromosomes. Successful separation between touching and overlapping chromosomes in a metaphase image is vital for correct classification. Current systems for automatic chromosome classification are mostly interactive and require human intervention for correct separation between touching and overlapping chromosomes. Since chromosomes are nonrigid objects, special separation methods are required to segregate them. Common methods for overlapping chromosomes separation between touching chromosomes tend to fail where ambiguity or incomplete information are involved, and so are unable to segregate overlapping chromosomes. The proposed approach treats the separation problem as an identification problem, and, in this way, manages to segregate overlapping chromosomes. This approach encompasses low-level knowledge about the objects and uses only extracted information, therefore, it is fast and does not depend on the existence of a separating path. The method described in this paper can be adopted for other applications, where separation between touching and overlapping nonrigid objects is required.