Although the role of phosphatases and antioxidant enzymes have been documented in phosphorus (P) deficiency tolerance, gene expression differences in the nodules of nitrogen fixing legumes should also affect tolerance to this soil constraint. In this study, root nodules were induced by Rhizobium tropici CIAT899 in two Phaseolus vulgaris recombinant inbred lines (RIL); RIL115 (low P-tolerant) and RIL147 (low P-sensitive) under hydroaeroponic culture with sufficient versus deficient P supply. Trehalose 6-P phosphatase and ascorbate peroxidase transcripts were localized within nodules in which O2 permeability was measured. Results indicate that differential tissues-specific expression of trehalose 6-P phosphatase and ascorbate peroxidase transcripts within nodules was detected particularly in infected zone and cortical cells. Under P-deficiency, trehalose 6-P phosphatase transcript was increased and mainly localized in infected zone and outer cortex of RIL115 as compared to RIL147. Ascorbate peroxidase transcript was highly expressed under P-sufficiency in the infected zone, inner cortex and vascular traces of RIL115 rather than RIL147. In addition, significant correlations were found between nodule O2 permeability and both peroxidase (r = 0.66*) and trehalose 6-P phosphatase enzyme activities (r = 0.79*) under sufficient and deficient P conditions, respectively. The present findings suggest that the tissue-specific localized trehalose 6-P phosphatase and ascorbate peroxidase transcripts of infected cells and nodule cortex are involved in nitrogen fixation efficiency and are likely to play a role in nodule respiration and adaptation to P-deficiency.