Modern sugarcane varieties are complex aneuploids and typically have chromosome numbers in the 100-125 range with about 5-10% of them contributed by wild relatives, mainly Saccharum spontaneum, and the rest by S. officinarum. This particular genomic constitution was found favorable for mapping the S. spontaneum genome, using maize as a diploid reference for comparison. We conducted an analysis of 32 individuals derived from the selfing of variety SP 701006 using four isozymes and 53 maize probes which covered the whole maize genome. A total of 348 segregating bands were generated. Highly significant cosegregations enabled us to place 94 markers into 25 cosegregation groups. Eighteen of these groups involved S. spontaneum specific markers and might therefore mark S. spontaneum chromosomes in segregation. On the basis of probes in common, the 25 cosegregation groups could be assembled into eight tentative linkage groups, of which seven describe S. spontaneum chromosomes. A large degree of synteny between sugarcane and maize could be inferred, with a much lower rate of recombination in sugarcane.