Since root endophytes may ameliorate drought stress, understanding which plants associate with endophytes is important, especially in arid ecosystems. Here, the root endophytes were characterized of 42 plants from an arid region of Argentina. Colonization by arbuscular mycorrhizal fungi (AMF) and dark septate endophytes (DSEs) was related to plant functional type (PFT), family, and phylogenetic relatedness. Overall, three main findings were observed. Firstly, only moderate levels of endophyte associations were found across all taxa (e.g., most Poaceae were not colonized by endophytes despite numerous accounts of colonization by AMF and DSEs). We determined 69% of plant taxa associated with some form of root endophyte but levels were lower than other regional studies. Secondly, comparisons by PFT and phylogeny were often qualitatively similar (e.g., succulents and Portulacineae consistently lacked AMF; variation occurred among terrestrial vs. epiphytic bromeliads) and often differed from comparisons based on plant family. Thirdly, comparisons by plant family often failed to account for important variation either within families (e.g., Bromeliaceae and Poaceae) or trait conservatism among related families (i.e., Rosidae consistently lacked DSEs and Portulacineae lacked AMF). This study indicates the value of comparing numerous taxa based on PFTs and phylogenetic similarity. Overall, the results suggest an uncertain benefit of endophytes in extremely arid environments where plant traits like succulence may obviate the need to establish associations.