The objective of this work was to identify molecular markers tightly linked to the gene controlling apospory in a hybrid population derived from a cross between apomictic Brachiaria brizantha and sexual Brachiaria ruziziensis. Since a maize chromosome 5 linkage group had previously been associated with the apomixis locus in Brachiaria we used twenty-five RFLP clones that map in detail maize chromosome 5 to cover systematically all syntenic regions of the hybrid genome. Forty-six AFLP markers were also generated. Three RFLP markers (detected by rz567, rz273, and cdo507 and two AFLP markers (PAM52-5 and PAM49-13) appeared to be related to the apo-region. Segregation data, together with previously reported data (corresponding to RFLP markers umc147, umc72, csu134, csu149 and RAPD marker OPC4) were used to generate a complete map of the region. Markers PAM52-5 and PAM49-13 were located respectively at 1.2 cM and 5.7 cM either side of the target locus. The map shows close synteny to regions of maize chromosome 5 and rice chromosome 2.