Background <p>An infant’s mother is one of the first sources of neonatal microbial colonization, and infant-maternal dyad microbial variations have been linked to childhood behavioral traits and mental health outcomes. However, how the gut microbiome influences mental health, including potential bidirectional relations between mother and child, remains poorly understood.</p> Method <p>Using metagenomic sequencing and behavioral questionnaires, we examined within-person and between-person (mother-infant dyad) associations between the gut microbiota and behavior across the first year of postnatal life (<i>N</i> = 121 dyads; <i>N</i> = 514 stool samples).</p> Results <p>There were rapid changes in taxa diversity and gut microbiota composition for infants, whereas the maternal microbiome remains relatively constant. Gut microbes and functional terms (e.g., antibiotic resistance genes and virulence factors)&#xa0;were associated with infant temperament but not maternal depression symptoms. Whereas maternal depression was not associated with any maternal taxa or functional terms.</p> Conclusions <p>Our findings provide evidence for complex within- and between-person relations between maternal and infant gut microbiomes and behavioral traits.</p> Impact <p><UnorderedList Mark="Bullet"> <ItemContent> <p>How the gut microbiome influences maternal mental health and infant behavior remains poorly understood.</p> </ItemContent> <ItemContent> <p>We measured mothers’ and infants’ gut microbiota composition and behavior across the first year of the infant’s life.</p> </ItemContent> <ItemContent> <p>Individual taxa from the infant, but not the maternal, gut were associated with infant behavioral temperament.</p> </ItemContent> <ItemContent> <p>Our findings provide evidence for complex bidirectional gut-behavior associations between mothers and infants.</p> </ItemContent> </UnorderedList></p>