Red clover persistence has been one of the major targets for the most breeding programs worldwide. A phenotypic characterization at above- and belowground level was performed to a set of highly persistent red clover populations. The objective was to identify phenotypic changes occurring after empirical selection for plant survival, which is the consensus criteria of persistence. Eleven red clover populations were established on mesocosms of polyvinyl chloride (PVC) tubes of 11 cm in diameter and 100 cm depth, containing as substrate a mixture (v/v) of sand, vermiculite, soil and perlite. The trial was organized in a randomized complete block design with four replicates, each replicate consisting of five mesocosms per population and one plant per mesocosm. In total, 220 mesocosms were handled. At aboveground level, growth parameters, specific leaf area (SLA) and shoot dry matter (ShootDM) were measured. At belowground level, root morphology (volume, diameter and length) and topology (altitude, external path length [EPL] and dichotomous branching index [DBI]) were measured through image analyses. Analyses of variance were performed implementing a phenotypic linear mixed model using the Restricted Maximum Likelihood method. Additionally, variance components were estimated and broad-sense heritability was calculated for each phenotypic trait. Highly persistent cultivars exhibited 30% higher ShootDM and 10% lower leaf size and SLA than the oldest low-persistent cultivar Quinequeli. At root level, they showed 20, 50 and 50% higher crown diameter, root length density and root volume than Quinequeli, respectively, but 20% lower DBI. Root traits exhibited medium-low values of genetic control; broad sense heritability ranged between 0.20 and 0.48. In conclusion, highly persistent red clover cultivars and experimental lines bred in Chile modified their phenotypic expression of individual plants at shoot and root levels relative to the oldest low persistent cultivar Quinequeli. Associations among above- and belowground traits offer opportunities for designing more efficient selection strategies. For instance, the strong relationship between SLA and root traits offers tremendous potential for indirect phenotypic selection.