An evaluation of 100 Eucalyptus globulus and 100 E. nitens trees (six years old) was made using the Pilodyn micro-drilling tool as an indicator of wood density. Thirty E. globulus and thirty E. nitens trees with high, medium and low density were selected and sampled with an increment borer at breast height for anatomical analysis using fibre tester equipment and the Resistograph device to generate detailed information about fibre biometry and anatomical wood properties of both species for hybrid development. Eucalyptus globulus trees had a basic wood density average of 478 kg/m3, while E. nitens had a density of 490 kg/m3. Both micro-drilling tools showed significant correlation coefficients with basic wood density. Correlation coefficients between basic wood density and Pilodyn values were negative, being -0.53 (p = 0.01) and -0.68 (p < 0.001) for E. globulus and E. nitens, respectively. For both species a positive correlation was observed between basic density and Resistograph mean amplitude; the correlation coefficient was 0.84 (p < 0.001) for E. globulus, and 0.85 (p < 0.001) for E. nitens. Eucalyptus nitens trees had a higher density and amplitude average and smaller Pilodyn values than E. globulus trees, while the latter had higher coarseness, fibre length and diameter at breast height than E. nitens trees. However, E. nitens showed larger differences between features of earlywood and latewood in a growth ring than E. globulus trees.