Acid soils include approximately 4 billion hectares of the earth's surface. Soils with pH < 5.6, deficiency of calcium, magnesium, phosphorous, molybdenum, iron, and Al saturation >35% with P level <16 parts per million are considered acidic for maize (Zea mays L.). Because of acid soils, fewer and smaller roots are produced, reducing the plant's capacity to uptake water and nutrients from the soil. The objectives of this study are to develop the marker linkage map for an acid soil tolerant maize F 2 segregating population, to dissect the quantitative trait loci (QTLs) for several traits, and to determine whether these QTLs could be used in a marker-assisted selection program for acid tolerance in maize. An F2 population of 221 individuals was genotyped at 118 SSR loci and 214 F3 families were evaluated in an alpha lattice design (22 x 10). The trials were grown in five environments, three acidic (V55, V65, and AYA65) and two normal fertile (PAL and TUR) in Colombia. Female flowering, male flowering, anthesis-silking-interval, yield, ears per plant, and plant and ear height were measured. Except for male and female flowering and anthesis-silking interval at AYA65, acid soil environments tended to have less the genetic variance. The estimates of heritabilities (h2) in acid environments were generally lower for all traits but yield in V65 (36%) and AYA65 (60%). The total length of the SSR linkage map was 1836.2 cM with a mean density of 15.56 cM. For all traits evaluated and based on the composite interval mapping analysis (LOD = 2.5), there were 66 QTLs identified for each environment. Thirteen QTLs were detected across acidic soils, 33 across normal-fertile soils, and 40 QTLs across all environments. In this study, no QTL with major effects were identified. QTLs had low single and total R2 values, for individual environments and across environments.