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Elevated levels of lipoprotein (a) [Lp(a)] are positively correlated with risk of cardiovascular disease and are thought to be a function of allelic variation in apo(a), the unique protein component of Lp(a). In this article we examine subspecies variation in Lp(a) levels and apo(a) isoforms in the baboon. Breeding populations of the five subspecies (Papio hamadryas hamadryas, P.h. cynocephalus, P.h. ursinus, P.h. papio, and P.h. anubis) of common long-tailed baboons are maintained at the Southwest Foundation for Biomedical Research. Serum samples were obtained from at least 20 unrelated animals of each subspecies. Twelve different size isoforms (including the null) o f apo(a) were identified across the five subspecies. These isoforms act as alleles; a maximum likelihood method was used to obtain the allele frequencies. Significant differences in apo(a) isoform frequencies were found between subspecies (X4 4 = 163.10, p < 0.0001). Quantitative levels of Lp(a) also differed among subspecies. We evaluated the correlation between genetic distances calculated using the quantitative Lp(a) levels and the apo(a) isoform data. Observed genetic relationships among the subspecies are consistent with the present-day geographic distribution and information from other marker protein systems. The findings indicate that the marker apo(a) may have great utility in both evolutionary and biomedical studies.