Many factors can affect the assembly of communities, ranging from species pools to habitat effects to interspecific interactions. In microbial communities, the predominant focus has been on the well-touted ability of microbes to disperse and the environment acting as a selective filter to determine which species are present. In this study, we investigated the role of biotic interactions (e.g., competition, facilitation) in fungal endophyte community assembly by examining endophyte species co-occurrences within communities using null models. We used recombinant inbred lines (genotypes) of maize (Zea mays) to examine community assembly at multiple habitat levels, at the individual plant and host genotype levels. Both culture-dependent and culture-independent approaches were used to assess endophyte communities. Communities were analyzed using the complete fungal operational taxonomic unit (OTU) dataset or only the dominant (most abundant) OTUs in order to ascertain whether species co-occurrences were different for dominant members compared to when all members were included. In the culture-dependent approach, we found that for both datasets, OTUs co-occurred on maize genotypes more frequently than expected under the null model of random species co-occurrences. In the culture-independent approach, we found that OTUs negatively co-occurred at the individual plant level but were not significantly different from random at the genotype level for either the dominant or complete datasets. Our results showed that interspecific interactions can affect endophyte community assembly, but the effects can be complex and depend on host habitat level. To our knowledge, this is the first study to examine endophyte community assembly in the same host species at multiple habitat levels. Understanding the processes and mechanisms that shape microbial communities will provide important insights into microbial community structure and the maintenance of microbial biodiversity.