Tropical forest trees are considered the largest component of the terrestrial biosphere carbon cycle. Yet, because of inaccessibility to root systems little is known about the coupling between canopy and roots, root biomass partitioning and its implication to root system respiration. Our objectives were: (1) evaluating root-canopy coupling and its potential underlying mechanisms, (2) quantifying root and shoot biomass partitioning and (3) quantifying respiration rates (Rr) of different root diameter classes (RDCs) in juveniles of two tropical tree species. We used a large aeroponics facility allowing direct access to the root systems. Simultaneous gas exchange measurements of leaves and fine roots (FR) under ambient and shade conditions showed a lagged response of FR respiration to photosynthesis in Khaya anthotheca (Khaya), while in Ceiba pentandra (Ceiba) the response was immediate. FR respiration under ambient light was higher and better coupled to canopy activity than FR respiration of shaded trees. Point dendrometers revealed a lagged response of bark width changes to photosynthesis in Ceiba. Results indicate that both immediate and lagged coupling patterns exist in Ceiba. In Khaya, only a lagged coupling was observed. More biomass was allocated to shoot in both species. Most of root biomass was allocated to very coarse roots (diameter>10 mm) in Ceiba, while in Khaya biomass was allocated more evenly between RDCs. The different partitioning between the two species may indicate different resource acquisition strategies. Specific Rr of FR was highest among all RDCs in both species. When up-scaled to total RDCs biomass it remained highest in Khaya and was only second to very coarse roots in Ceiba. The inconsistency between Rr of RDCs between the two species calls for cautious modeling. Our study improves understanding of carbon dynamics in tropical trees: the potential mechanisms underlying root-canopy coupling; whole-tree biomass partitioning; and respiration by various root categories.