In the southwest of the Iberian Peninsula, Phytophthora cinnamomi Rands is causing irreversible damage to populations of the two most common species of Quercus, the holm oak (Quercus ilex L.) and the cork oak (Quercus suber L.). Although the symptoms are similar in the two species, the mortality rates are different. We found significant differences in the post-infection growth of the root system as a function of tree species, as well as initial plant size, and inoculum level. We observed a marked decrease in the growth of new roots in Q. ilex with increasing inoculum level, while in Q. suber, we found longer but thinner roots with a moderate inoculum level. In both species, we observed a worsening in the water status of the plants from the lowest inoculum level.