We have developed an algorithm which combines data obtained from restriction digestion experiments and hybridization experiments to construct robust physical maps of whole chromosomes. The algorithm has been incorporated into a program which accepts hybridization data consisting of an unordered hybridization matrix and fingerprinting data containing band coordinates for each clone. The combined data is used to produce a non-redundant, ordered matrix which can be further reduced to represent a minimum tile coverage of the chromosome. In addition, the method also takes into account multi-level hybridization events which allows for an improved treatment of the hybridization data. The program is evaluated against several other contig building programs using simulated and real data sets. Finally, it is applied to construct a physical map of the 4.1 Mb genome of Ochrobactrum anthropi based on 1387 clones and 70 probes, as well as 624 fingerprints.