Background: Alterations in bacteria that naturally reside in the intestines may contribute to obesity. Because the infant microbiota are largely derived from the mother, differences in the maternal microbiota may link maternal and child obesity. Methods: This study included 77 mother–child pairs, with children assessed at ∼2years of age. Women completed measures of maternal health, child diet and collected stool samples from their children which were analyzed by deep sequencing. Shannon Diversity Index (SDI) was used to measure alpha-diversity and the adonis statistic was used to measure differences in distance matrices between variables. Results: Children born to obese mothers had a significantly higher SDI (p<0.05), indicating greater bacterial diversity, and a different microbiota community structure based on adonis (p<0.05). Higher maternal BMI predicted greater prevalence of Faecalibacterium, Oscillibacter, and Roseburia in the child. These effects were not attributable do differences in child body composition. Obese and non-obese mothers were demographically similar and showed no significant differences in child feeding behavior. Conclusions: Maternal obesity may predict differences in the gut microbiota of offspring. In particular, we observed greater Faecalibacterium and Oscillibacter in toddlers, microbial populations that have previously been associated with obesity. This may be a mechanism by which maternal obesity confers risk of obesity in offspring.