Comparative analyses have sought to explain variation in human marriage patterns, often using predictions derived from sexual selection theory. However, most previous studies have not controlled for non-independence of populations due to shared ancestry. Here we leverage a phylogenetic supertree of human populations that includes all 186 populations in the Standard Cross-Cultural Sample (SCCS), a globally representative and widely-used sample of human populations. This represents the most comprehensive human phylogeny to date, and allows us not only to control for non-independence, but also to quantify the role of population history in explaining behavioral variation, in addition to current socio-ecological conditions. We use multiple imputation to overcome missing data problems and build a comprehensive Bayesian phylogenetic model of marriage patterns with two correlated response variables and eleven minimally collinear predictors capturing various socio-ecological conditions. We show that ignoring phylogeny could lead to both false positives and false negatives, and that the phylogeny explained about twice as much variance as all the predictors combined. Pathogen stress and assault frequency emerged as the predictors most strongly associated with polygyny, which had been considered evidence for female choice of good genes and male intra-sexual competition or male coercion, respectively. Mixed support was found for a polygyny threshold based on variance in male wealth, which is discussed in light of recent theory. Barring caveats, these findings refine our understanding of the evolution of human marriage systems, and highlight the value of combining population history and current socio-ecology in explaining human behavioral variation. Future studies using the SCCS should do so using the present supertree.