A method for tracking specific in situ hybridizations in biological samples using molecular barcodes is disclosed. Present invention specifically addresses the in suspension in situ hybridization protocols and makes it possible to track a mixed sample processed on a high throughput flow cytometer. Since the DNA probes selected for the molecular barcodes are naturally existing sequences on the chromosomes, each cell will have two copies of the molecular barcode as opposed to the single barcode provided by the other systems. Tracking is accomplished by following the florescence patterns emitted by the two, three, four or five fluorescent tags attached to the DNA probes. Alternatively, colorimetric system can be used for tracking by employing non-fluorescent tags and subsequent specific enzyme-substrate reactions.