The lack of resistance to bacterial diseases increases both the financial cost and environmental impact of tomato (Lycopersicon esculentum Mill.) production while reducing yield and quality. Because several bacterial diseases can be present in the same field, developing varieties with resistance to multiple diseases is a desirable goal. Bacterial spot (caused by four Xanthomonas Dowson species) and bacterial speck (caused by Pseudomonas syringae pv. tomato Young, Dye and Wilkie) are two economically important diseases of tomato with a worldwide distribution. The resistance gene Pto confers a hypersensitive response (HR) to race 0 strains of the bacterial speck pathogen. The locus Rx3 explains up to 41% of the variation for resistance to bacterial spot race T1 in field trials, and is associated with HR following infiltration. Both Pto and Rx3 are linked in repulsion phase on chromosome 5. We made a cross between two elite breeding lines, Ohio 981205 carrying Pto and Ohio 9834 carrying Rx3, to develop an F2 population and subsequent inbred generations. Marker-assisted selection (MAS) was applied to the F2 progeny and to F2:3 families in order to select for coupling-phase resistance. Thirteen homozygous progeny from 419 F2 plants and 20 homozygous families from 3716 F3 plants were obtained. Resistance was confirmed in all selected families based on HR in greenhouse screens using bacterial speck race 0 and bacterial spot race T1 isolates. Resistance to bacterial spot race T1 was confirmed in the field for 33 of the selected families. All selected families were also resistant to bacterial speck in the field. MAS was an efficient tool to select for desirable recombination events and pyramid resistance.