Terrestrial plants can harbor endophytic fungi that may induce changes in plant physiology that in turn affect interactions with herbivorous insects. We evaluated whether the application of entomopathogenic fungi Beauveria bassiana and Metarhizium brunneum to soybean seeds could become endophytic and affect interactions with soybean aphid (Aphis glycinesMatsumura). It was found that A. glycines population sizes increased on plants with M. brunneum (strain F52) seed inoculum, but no significant effects were shown with analogous treatments with B. bassiana (strain GHA). Fungi recovered from soybean plant tissues indicate that endophytism was established, and that B. bassiana was more prevalent. Metarhizium brunneum was only recovered from stems, but B. bassiana was recovered from stems and leaves. This work confirms that some entomopathogenic fungi can be endophytic in soybean, however, some of these fungi may have a negative effect on the plants by increasing susceptibility of soybean to A. glycines. We also used DNA sequence data to identify species of Metarhizium obtained from agricultural fields in Iowa. Phylogenetic analyses, based on DNA sequence data, found that all isolates were Metarhizium robertsii, which is consistent with past studies indicating a cosmopolitan distribution and wide host range for this species. These results are important for understanding the dynamics of implementing environmentally sustainable measures for the control of pest insects.