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<i>Phytophthora nicotianae</i> (<i>P.n</i>.) causes root rot of citrus, damaging the fibrous roots, depleting carbohydrate reserves, and reducing water and nutrient uptake capacity. Huanglongbing (HLB) is a systemic citrus disease, caused by phloem-limited <i>Candidatus </i>Liberibacter asiaticus (Las), that damages fibrous roots and disrupts photosynthate production and transport. To investigate how Las and <i>P.n.</i> cause root decline, Swingle citrumelo rootstock seedlings were inoculated with Las or <i>P.n.. </i>Root systems of all seedlings were trimmed at the time of <i>P.n.</i> inoculation to induce root growth. Roots were separated into diameter classes, and biomass and root length were measured. Las caused more total root loss than <i>P.n.</i> by 11 weeks post inoculation (wpi), 32% and 12%, respectively. <i>P.n.</i> caused greater damage to fibrous roots from 0 to 1.2mm diameter by 11 wpi. Compared to healthy seedlings, Las- or <i>P.n.</i>-infected seedlings at 5 wpi produced more or less length of new roots, respectively, suggesting that after the early stage of infection Las stimulated and <i>P.n.</i> inhibited root growth. Las induced root loss was evident at 11 wpi. Lower total leaf area by 11 wpi indicated that canopy decline followed root loss. In conclusion, Las stimulated root growth at the early stage of HLB development, which reduced carbohydrate status and canopy production at a more advanced stage of disease.