Phosphorus (P) deficiency is a major limiting factor for crop production in several countries. A better understanding of the genetic components of P use efficiency (PUE) is required to improve crop performance in low-P soils. To date, no QTLs (quantitative trait loci) were mapped for PUE using grain yield and other late phenotypic data in tropical conditions. Thus, we evaluated the genetic architecture of PUE in tropical maize (Zea mays L.) using multiple interval mapping for design III in a population of 140 RILs (recombinant inbred lines) backcrossed with both parental lines. The parental lines contrasted for yield and for PUE, a phenotypic index that was further decomposed into P acquisition efficiency (PAE) and P utilization efficiency. Our results showed that dominance effects were more important than additive effects for explaining the variations in PUE and its components. Approximately 80% of the QTLs mapped for PAE co-localized with those for PUE, indicating that the efficiency in acquiring P is the main determinant of PUE in tropical maize. Also, QTLs for PUE and PAE were located near to candidate genes previously associated with root development. Thus, we present important information to guide breeding strategies for the development of maize cultivars more adapted to P deficiency.