A genetic linkage map was constructed for Pacific yew (Taxus brevifolia Nutt.) based on random amplified polymorphic DNA (RAPD) markers. A series of optimization experiments were conducted to develop a highly repeatable protocol for Pacific yew. In these experiments, a high MgCl2 concentration (5.5 mM) together with a low primer concentration (0.2 mu m) in the polymerase chain reaction (PCR) mixture yielded the best amplification products. PCR amplification products were further improved by treating the template DNAs with RNase. Experiments showed that bovine serum albumine had the same effect as RNase on PCR amplification. The segregating mapping population consisted of 39 haploid megagametophytes from a single mother tree. DNA extracted from a subset of 6 megagametophytes was screened with 345 ten-base oligonucleotide primers of arbitrary sequence. Of the screened primers, 28% revealed at least one polymorphic locus. Eighty-six of these primers revealed at least one polymorphic locus and were used with the entire set of megagametophyte DNAs. One-hundred-two loci were scored and segregated in the expected 1.1 ratio (1.19 locus per primer). Linkage analysis was conducted using MAPMAKER. Forty-one of 102 markers were distributed into 17 linkage groups and covered 305.8 centimorgans. The remaining 61 unlinked markers should be assigned to linkage groups as more markers are added to the map.