Pinus oocarpa is the most important conifer for resin production in Mexico, so superior resin trees were selected in the Southern Mountains of Oaxaca, Mexico. The objective was to determine the variation and differences among provenances and among trees according to the parameters of seedling emergence and the number of cotyledons, and their relationship with elevation and climatic variables. The seedling emergence of four replicates of 20 seeds from 80 trees was counted daily. For the emergence parameters, provenance contributed 42.02% to the total variance, tree 29.19% and error 28.79%. Only tree (11.71%) and error (88.29%) contributed to the total variance of the cotyledon number. The effect of provenance (p ≤ 0.0006) and tree (p ≤ 0.0001) was significant for all variables evaluated. Higher-elevation provenances and trees had higher emergence values. The emergence parameters were positively associated with tree elevation. Climatic variables related to precipitation and temperature were negatively related to the emergence parameters. The results allow for the selection of phenotypes without emergence problems to establish seed orchards.