Selecting clones with the best genetic material is one goal of eucalyptus breeding programs. Understanding the variations between the wood from different hybrid clones during drying is necessary to process improvement. This study aimed to select eucalyptus clones for lumber production based on their drying defects. From a plantation in Brazil, 42 trees within the seven different clones were used. All trees were 13 years old. The effect of the genetic material on the apparent density of the clones was significant. It was possible to separate the clones into four groups. Even if the wood was from the same genotype, a load of boards made from Eucalyptus grandis × Eucalyptus urophylla wood exhibited heterogeneity in the drying rate due to factors inherent in the wood, especially the apparent density. The apparent density negatively affected the drying rate of the clones, i.e., approximately 70.5% of the drying rate was explained by the apparent density. Denser pieces exhibited lower drying rates. For a more homogeneous natural drying, it is recommended that the composition of the stacks use pieces with the same apparent density and thus similar initial moisture. The air-drying process is recommended to release any free water from eucalyptus woods.