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<i>Oxytropis</i> plants are widely distributed in the grasslands in northern China. Some <i>Oxytropis</i> species have been reported to contain the mycotoxin swainsonine, an alkaloid which causes poisoning in livestock, referred to as locoism. Previous studies showed that endophytic fungi (<i>Alternaria</i> <i>oxytropis</i>) symbiotically associate with these <i>Oxytropis</i> species to produce swainsonine. However, the influence of variation within the <i>Oxytropis</i> genus on the fixation or loss of symbiosis and toxicity is poorly understood, as is the influence of environmental factors. Here we used a collection of 17 common <i>Oxytropis</i> species sampled in northern China to assess genetic diversity using genotyping by sequencing which was compared with the levels of the endophyte and swainsonine. Results showed that nine <i>Oxytropis</i> species have detectable <i>A.</i> <i>oxytropis</i> colonisation, and seven <i>Oxytropis</i> species contain sufficient swainsonine to be considered poisonous, whereas the rest may be non-toxic. Species variation rather than the genetic lineage was associated with the fixation or loss of endophyte and swainsonine production, which appears to have resulted from genetic drift. Genotype × Environment (G × E) effects were also found to influence endophyte and swainsonine levels amongst species of the <i>Oxytropis</i> genus. Our study will provide a better understanding about the evolutionary basis of <i>A.</i> <i>oxytropis</i> symbiosis and swainsonine biosynthesis in locoweeds.