Humans are host to a multitude of microorganisms that rapidly populate the body at birth, subject to a complex interplay that is dependent on host genetics, lifestyle, and environment. The host-associated microbiome, including the oral microbiome, presents itself in a complex ecosystem important to health and disease. As the most common chronic disease globally, dental caries is induced by hostmicrobial dysbiosis in children and adults. Multiple biological and environmental factors are likely to impact disease predisposition, onset, progression, and severity, yet longitudinal studies able to capture these influences are missing. To investigate how host genetics and environment influenced the oral microbial communities over time, we profiled supragingival plaque microbiomes of dizygotic and monozygotic twins during 3 visits over 12-months. Dental plaque DNA samples were amplified by targeting the 16S rRNA gene V4 region, and microbial findings were correlated with clinical, diet and genetic metadata. We observed that the oral microbiome variances were shaped primarily by the environment when compared to host genetics. Among the environmental factors shaping microbial changes of our subjects, significant metadata included age of the subject, and the age by which subjects initiated brushing habits, and the types of actions post-brushing. Relevant heritability of the microbiome included Actinomyces and Capnocytophaga in monozygotic twins and Kingella in dizygotic twins. Corynebacterium and Veillonella abundances were associated with age, whereas Aggregatibacter was associated with younger subjects. Streptococcus abundance showed an inverse association over time, and Selenomonas abundances increased with brushing frequency per day. Unraveling the exact biological mechanisms in caries has the potential to reveal novel host-microbial biomarkers, pathways, and targets important to effective preventive measures, and early disease control in children. Across various human body habitats, including the oral cavity, mutually beneficial relationships between the host and its microbiome lead to homeostatic phenotypic patterns. While shifts in gastrointestinal 1,2 and skin 3-5 habitats have advanced our understanding of host-microbial dysbiosis, the oral counterpart has not received the same level of mechanistic interrogation, particularly with respect to host genetics link. One central question remaining unanswered is the extent to which differences in the microbiome are explained by host genetics. As one of the most diverse microbial ecologies in humans, the oral microbiome has critical importance to local oral and systemic health. In fact, oral microbial dysbiosis underlies many human oral diseases with systemic consequences, but the exact mechanism regulating microbial patterns associated with health to disease transition and from acute to chronic lesions remains elusive. Loss of host-microbial homeostasis in the oral habitat leads to dysbiosis and a range of oral and systemic conditions, including caries, periodontal diseas...