Controlling coffee nematodes using fewer pesticides is a priority for most producing countries. The aim of this study was to identify ecological and agricultural factors associated with Meloidogyne exigua and Pratylenchus coffeae sensu lato population densities in coffee roots. The influence of these factors was studied in a two-year survey by characterizing 57 coffee plots in five major producing regions in Costa Rica, where coffee is generally cultivated in intensified systems. Correspondence analyses and Chisquared automatic interaction detector (CHAID) classification trees were used to identify and classify the ecological and agricultural factors associated with nematode population densities. M. exigua and P. coffeae population densities were opposites with respect to soil characteristics. Low M. exigua population densities were especially found in soils with low sand and high Zn and K contents. The opposite was seen for P. coffeae. In addition, M. exigua and P. coffeae seemed to have different climatic requirements: M. exigua was mainly found at lower altitudes than P. coffeae. Consequently and through possible competition phenomena between P. coffeae and M. exigua, a negative correlation was found between the two nematode population densities on a plot scale. We found only one cropping practice that seemed to affect both nematodes similarly: a within-row distance between coffee trees of less than 0.9 m was associated with large M. exigua and P. coffeae population densities. The results of this study provide further evidence of the greater intensity of pest and disease attacks in intensified coffee systems.