We studied genetic polymorphism and phylogeny using nuclear random amplified polymorphic DNA markers (RAPDs) and mitochondrial DNA (mtDNA) restriction fragment length polymorphisms (RFLPs) in the three California Closed-Cone Pines: Pinus attenuata Lemm., P. muricata D. Don, and P. radiata D. Don. A total of 343 to 384 trees derived from 13 populations were analyzed using 13 mitochondria' gene probes and two restriction enzymes, and more than 90 RAPD loci generated by 22 primers. Southern hybridization was used to test homology among comigrating RAPD markers. Segregation analysis and Southern hybridization were carried out to distinguish between RAPD fragments of nuclear and organellar origin. Estimates of genetic diversity and population differentiation, and phylogenetic analyses based on RAPD and RFLP markers, were compared with those based on allozymes from a similar study. Twenty-eight distinct mtDNA haplotypes were detected among the three species. All three species showed limited variability within populations, but strong differentiation among populations. Based on haplotype frequencies, genetic diversity within populations (Hs) averaged 0.22, and population differentiation (GsT and 0) exceeded 0.78. Analysis of molecular variance (AMOVA) also revealed that more than 90% of the variation resided among populations. Species and populations could be readily distinguished by unique haplotypes, often using the combination of only a few probes. Twenty-eight of 30 (93%) comigrating RAPD fragments tested were homologous by Southern hybridization. Hybridization with enriched mtDNA, and chloroplast DNA (cpDNA) clones, identified one fragment as being of mtDNA origin and two as being of cpDNA origin, among 142 RAPD fragments surveyed. RAPD markers revealed moderately higher intrapopulation gene diversity and significantly higher total genetic diversity and population differentiation than did allozyme markers for each species. Simulation analysis to study effects of dominance on RAPD diversity suggested that dominance substantially depressed values of diversity within populations and inflated values of differentiation among populations. By comparison to our empirical analyses, we inferred that the underlying diversity of RAPD markers is substantially greater than that of allozymes. Results of phylogenetic analysis of RAPD markers were largely consistent with those from allozyme analysis, though they had many minor differences. Joint phylogenetic analysis of both the RAPD and allozyme markers strongly supported a common ancestor for P. radiata and P. attenuata, and south to north migration histories for all three species. Dendrograms based on mtDNA analysis, however, strongly disagreed with those based on allozymes, RAPDs, chloroplast DNA and morphological traits, suggesting convergent genome evolution.