This study aimed to assess the effect of smoking different tobacco types on the supragingival microbiome and its relation to dental caries. Forty supragingival plaques were collected from smokers of a single tobacco type and non-smokers seeking treatment at the University Dental Hospital Sharjah, UAE. DMFT (decayed, missing and filled teeth) was determined for all participants who were divided into two groups: no-low caries (NC-LC: DMFT= 0-4; n=18) and moderate-high caries (MC-HC: DMFT= 5-20; n=22). 16S rRNA gene was sequenced using third-generation sequencing with Nanopore technology. Microbiome composition and diversity were compared. Caries were most common among cigarette smokers. Supragingival microbiota were significantly altered among smokers of different tobacco types. In cigarette smokers, cariogenic bacteria from genus Streptococcus (including S. mutans) were significantly more among subjects with NC-LC, while Lactobacilli (including L. fermentum) were more among subjects with MC-HC. In medwakh smokers, several periodontopathogens were significantly elevated in subjects with NC-LC, while other pathogenic bacteria (as Klebsiella pneumoniae) were more in those with MC-HC. Cigarette and alternative tobacco smoking had a significant impact on the supragingival microbiome. Dysbiosis triggered by smoking can be a predisposing factor to caries. Tobacco cessation and oral health-promoting strategies are required to prevent dental caries when the oral microbiome is disturbed.