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Key message: Hybrid seed production in adjacent seed orchards of Acacia auriculiformis and Acacia mangium was influenced by (i) flowering times of the two species and (ii) the distances of parent trees from the inter-orchard boundary. Approximately 80% of hybridisation events were found within 60 m from the boundary. Context: Understanding pollen dispersal has important implications for breeding and seed production of pure species and hybrid Acacia. Aims: We examined patterns of hybrid production in adjacent clonal seed orchards of A. auriculiformis and A. mangium in Vietnam. Methods: We assessed the frequency of hybrid offspring using four species-diagnostic SSR markers in seed collected from a total of 72 trees (75 seedlings per tree) at distances ranging from 4 to 144 m from the inter-orchard boundary. The number of hybrid was determined from SSR allele peak sizes in pooled sample (10 seedlings per pool, 540 pools). Calibrations were developed from pools with known proportions of pure-species and hybrid material. Results: Hybrid frequency differed significantly among individual clones (P < 0.001) but not between species (A. mangium = 3.4%, A. auriculiformis = 2.8%). Two late-flowering clones of A. auriculiformis yielded no hybrids. The level of interspecific hybridisation declined significantly (P < 0.001) with increasing distance, and no hybrid seed was produced by trees located more than 116 m from the inter-orchard boundary. Conclusion: Pooling of tissue samples for analysis of species-specific DNA polymorphisms was an efficient, low-cost strategy for detecting hybrid genotypes among the offspring of pure-species parents, and a low rate of associated error was demonstrated. The inferred decline in inter-species pollen flow with increasing distance from the boundary between the two orchards provides guidance for the design of hybridising orchards and isolation requirements to prevent contamination of seed orchards by external pollen sources. [ABSTRACT FROM AUTHOR]