The gut microbiota is influenced by multiple factors, including diet. In studies of non-pregnant groups, the composition of the gut microbiota in vegetarians has higher abundance of bacteria that are associated with anti-inflammatory properties and lower levels of pro-atherogeneic metabolites in the host. The impact of a vegetarian diet on gut microbiota in pregnancy has not been examined. This study evaluated the gut microbiota composition at 16 weeks gestation in all (N=9) vegetarian women and 18 omnivores matched for BMI, future gestational diabetes status and energy intake from faecal samples at 16 weeks gestation from the SPRING (Study of PRobiotics IN Gestational diabetes) RCT by 16S rRNA sequencing. Sequencing data was analysed with the QIIME and Calypso software tools. Vegetarian women reported significantly lower protein, sugar and saturated fat intake but higher polyunsaturated fat intake than matched omnivorous women. The beta diversity of the gut microbiota diversity was higher in vegetarian women but alpha diversity was not affected. The gut microbiota of vegetarian women showed higher abundance of the carbohydrate-fermenter Bacteroides, the butyrate producers Roseburia and Clostridium but lower abundance of the lactose-user Collinsella and of Odoribacter. Protein intake was negatively correlated with Bacteroides and Roseburia abundance whereas polyunsaturated fat intake was negatively correlated with Collinsella abundance but positively with Bacteroides. Saturated fat and sugar intake were negatively correlated with Roseburia abundance. Sugar intake was also negatively correlated with Bacteroides abundance but positively with Odoribacter abundance. In summary, this analysis describes differences in macronutrient intake between vegetarians and omnivores which are associated with changes to the abundance of specific genera in their gut microbiota. These changes are consistent with studies outside pregnancy suggesting that vegetarian compared to omnivorous diets result in increased Bacteroidetes, Prevotella and Clostridium species – bacteria which can engage in polysaccharide degradation and fermentation.