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Background Smoking prevalence varies over time and place due to various social, environmental and policy influences. However, its spatio-temporal patterns at small-area level are poorly understood. This paper attempts to describe spatio-temporal patterns of adult (age?>?18) and youth (age 12-18) smoking prevalence at the municipality level in Ontario, Canada and identify potential socio-demographic, environmental, and policy factors that may affect the patterns. Methods Multilevel temporal and spatio-temporal models were fitted to the Canadian Community Health Surveys (2000-2008) data. In total, approximately 160,000 respondents 12 years of age and over living in Ontario were used for this analysis. Results The results indicate that during the time period 2003-2008, age-sex stratified smoking prevalence dropped for both the adult and youth populations in Ontario. The tendency is more obvious for youth than for adults. Smoking restriction at home is a leading factor associated with the decline of adult smoking prevalence, but does not play the same role for youth smoking. Despite the overall reduction, smoking prevalence varies considerably across the province and inequalities among municipalities have increased. Clusters of high and low smoking prevalence are both found within the study region. Conclusion The identified spatial and temporal variations help to indicate problems at the local level and suggest future research directions. Identifying these variations helps to strengthen surveillance and monitoring of smoking behaviours and the evaluation of policy and program development at the small-area level.