Pigeon pea is an important source of protein for smallholder farmers in South Africa. The average seed yield per hectare ranges from 0.5 to 1 tonne due to the use of un-improved varieties that succumb to both biotic and abiotic stresses. Understanding the relationship between seed yield and agronomic traits in a genetically diverse germplasm collection is a prerequisite for developing an efficient selection and breeding program. This study determined the relationship between seed yield and agronomic traits to identify key traits for selection. Two separate experiments involving seven short and six medium duration pigeon pea genotypes were planted in a randomized complete block design (RCBD), each with three replications. Agronomic traits, including yield and its components’ genotype mean data was subjected to correlation, path coefficient and stepwise regression analyses. The results showed a strong positive and significant correlation between number of pods per plant and seed yield in both medium and short duration genotypes. The number of pods per plant had a high direct effect on seed yield in both medium and short duration with values of (0.43) and (0.63) respectively. Number of branches and pod length exhibited high direct effect (0.30-0.99) for medium duration. However, seed yield per plant was an important predictor of seed yield in short duration while seed yield per plant, 100 seed weight and number of seeds per pod were key predictors of seed yield in medium duration genotypes. Therefore, these traits should be targeted for seed yield improvement in Pigeon pea.