Serratia marcescens IRBG500 and Herbaspirillum seropedicae Z67 grow endophytically in rice. The ability of these bacteria to colonize rice grown under increased nutrient availability was assessed in variety IR72 using strains marked with transposon-based gusA. The endophytic colonization was monitored via bacterial enumeration and histochemical visualization of GUS expression of bacteria in plant tissues. Rhizoplane and endophytic colonization by both bacteria was significantly inhibited in the rice plants grown in the presence of 10 mM $NH_4Cl$. In contrast, the addition of 10 mM $KNO_3$ showed no adverse effect on colonization. Increasing the concentration of $Ca^{2+}$ to 5 mM significantly reduced endophytic colonization by both bacterial strains, whereas the addition of 0.5 mM $Fe^{2+}$ substantially lowered the colonization of roots by S. marcescens IRBG500 but showed no effect on colonization by H. seropedicae Z67. Taken together, these finding suggest that, like in legume-rhizobial symbiosis as well as plant-pathogen interactions, nutrient status, particularly $NH_4^+$ and $Ca^{2+}$ concentrations in the surrounding medium, plays an important role in the regulation of endophytic infection and colonization processes in rice.