The breeding potential of reindeer husbandry is determined by competent work with genetic resources; therefore, the study of the phenotypic traits of reindeer must be carried out in combination with the study of the features of their gene pools. In this work, we analysed the correlations and genetic associations of phenotypic traits in 98 female reindeer (Rangifer tarandus) of the Nenets breed aged from 3 to 9 years in a comparative aspect according to the main body measurements and physique indexes calculated from these measurements. A panel of 16 microsatellite loci (BMS1788, RT30, RT1, RT9, C143, RT7, OHEQ, FCB193, RT6, C217, RT24, C32, BMS745 NVHRT16, T40 and C276) was used for analysis. The search for associations between the genotype and phenotype of reindeer was performed using regression analysis; only for three phenotypic traits, height at the withers, chest depth and the index of prolixity, non-zero heritability was revealed. Using correlation analysis, it was found that the live weight of adult females, taking into account age and genetic relationship, has a high positive correlation with the height at the withers (r ≈ 0.70), chest girth (r ≈ 0.79) and chest depth (r ≈ 0.73).