Technical Abstract: Some species of black-spored aspergilli (Aspergillus section Nigri) are able to cause disease in several plant hosts, including peanut and maize seedlings. Besides the economical impact of black-spored aspergilli infections, several species within this section are well known mycotoxin producers, specifically the teratogenic, nephrotoxic, and potential carcinogenic ochratoxin A. The interactions between maize and A. section Nigri species are poorly understood, especially since endophytic colonizations are symptomless. In this study, A. carbonarius and A. foetidus were transformed with green, yellow, and red fluorescent proteins, and used to measure colonization of maize seedlings under drought stress conditions. Maize kernels were infected with 5 × 104 spore/ml suspension. After 3 weeks of inoculation, seedlings were drought stressed, and the colonization of lateral roots, meristem, and stems was monitored at different time points with the aid of laser scanning confocal microscopy. The use of a fluorescent tagging approach determined the different colonization patterns employed by black spored aspergilli species during maize seedling colonization.