Neltuma pallida (algarrobo) is a characteristic tree species of the Peruvian tropical dry forest that plays an essential ecological role while facing increasing pressure from habitat degradation and unsustainable exploitation. Identifying superior genetic resources is therefore fundamental for long-term conservation and breeding initiatives. This study evaluated the phenotypic diversity of natural N. pallida populations in the Piura and Tumbes regions of northern Peru to identify elite trees with desirable traits. A stratified random sampling approach was implemented across 13 localities, where 631 mature trees were assessed. Measurements included dendrometric and reproductive characteristics, complemented by environmental information derived from soil analyses, climatic records, topographic variables, and geographic information systems. Population differentiation was quantified using the phenotypic differentiation index (PST), allowing the comparison of within- and among-population variability. Considerable phenotypic variation was observed among populations, with significant differences in tree size and fruit productivity associated mainly with environmental conditions, particularly soil fertility and organic matter content. The high PST estimates (0.83–0.98) indicated pronounced population divergence, suggesting adaptive differentiation across the studied environments. Based on a multi-trait evaluation, eight outstanding trees were selected as promising candidates for germplasm conservation and future genetic improvement programs. These findings contribute valuable information for the sustainable conservation, management, and utilization of N. pallida genetic resources in Peru's arid dry forest ecosystems.