Potato zebra chip caused by Candidatus Liberibacter solanacearum (CLso) was originally discovered in Mexico in 1994, and identified in New Zealand in 2008. It caused severe economic impacts to the potato industries in North America. CLso infects Solanaceous and Apiaceous crops, such as tomato, carrot, pepper, eggplant, tobacco, celery and etc. To date, eleven haplotypes (A-H,U, Cras1 and Cras2) of CLso have been identified with or without obvious variations in pathogenicity among them. For instance, CLso haplotype B is lethal to both potato and tomato, while haplotype A is lethal to potato but not to tomato. We present data to underlie the mechanism of CLso pathogenicity by analyzing the transcriptomic response of tomato plants to CLso haplotypes A and B. In total, 9913 transcripts were analysed, among which, 138 genes are upregulated, and 331 genes are downregulated, comparing haplotype B to A. Healthy tomato plants and plants infected by haplotype A have similar expression levels, which is consistent with the fact that CLso haplotype A does not show obvious symptoms on tomato plants (cv moneymaker). GO enrichment analysis indicates that CLso haplotype B significantly affects hosts’ carbohydrate metabolism, cell wall organization or biogenesis, and hydrolase activities. Starch accumulation is significantly affected in plants infected by pathogenic CLso. Specifically, genes related to photosynthesis were generally downregulated in tomato plants infected by CLso haplotype B. As the result, carbon fixation is compromised. Concurrently, enzymes catalyzing the biosynthesis of starch from glucose are also downregulated, while amylolysis genes are upregulated. The alternations indicate that carbohydrate consumption in infected tomato plants is significantly greater than accumulation, which may explain the formation of zebra chip symptoms in potato. Potato tubers infected by CLso caused the conversion of potato starch to water-soluble sugars, which develop discoloration along the vascular tissue, turning the chips to unsightly dark blotches, stripes, or streaks after cooking. Understanding the pathogenicity and virulence mechanism of CLso may enhance the disease control and create opportunity for breading resistant or tolerant varieties.