Phenotypic variation in phenological, quantitative and qualitative traits was assessed in geographically-isolated, farmer-managed wheat landrace populations grown under subsistence farming conditions. Several multivariate, genetic diversity and structural equation modeling procedures were used to build a comprehensive structure of the landrace and to (1) identify and construct multivariate distances between components of the landrace, (2) identify plant- and seed-related traits contributing to its composition, (3) build principal components that can account for maximum variation, (4) quantify variance components accounted for by major seed qualitative traits, (5) partition total diversity and estimate levels of population differentiation, (6) build and validate a predictive model of landrace population-trait association, (7) identify traits affecting spikelet fertility as a critical component of grain yield under the prevailing hot conditions in Oman, and (8) construct and interpret structural equation models to estimate the direct and indirect effects of quantitative and qualitative traits on grain yield per plant for each landrace population. The results will be discussed within the context of on-farm conservation and sustainable utilization of endangered wheat landrace populations under subsistence farming and to illustrate the use of advanced multivariate statistical methods in assessing phenotypic variation in subdivided landrace populations.