A five-year experiment was initiated in 2000 to measure the impact of alternative land management practices on soil health in fresh market tomato production. Land management practices consisted of: (1) conventional tomato production using soil fumigation with 1,3-dichloropropene plus chloropicrin, (2) organic production using cover crops of Sunn Hemp (Crotalaria juncea) and Japanese Millet (Echinochloa crusgalli var frumentacea) combined with annual applications of poultry manure and urban plant debris, (3) weed fallow, (4) disk fallow, and (5) establishment of bahiagrass (Paspalum notatum) pasture. This study reports changes in soil bacterial communities after multiple years of alternative practices and following the initiation of tomato production. Length Heterogeneity PCR (LH-PCR) and Terminal Restriction Fragment Length Polymorphisms (T-RFLP) were used to analyze soil bacterial 16S rDNA, and uni- and multivariate analyses of amplicon profiles were employed to discriminate the soil bacterial communities under different land management practices. LH-PCR using primer pairs 27-355 discriminated soil bacterial communities subjected to the different land management practices. T-RFLP was more sensitive to the selection of primers and restriction enzymes. For example, T-RFLP using the primer 357 and restriction enzyme Alu1 distinguished the bacterial communities in organic from other management programs, but was not as effective as LH-PCR in distinguishing the bacterial communities under the other four treatments; while T-RFLP using primer 1387 and restriction enzyme Alu1 was unable to discriminate bacterial communities. Based on univariate analysis, Shannon's diversity indices of LH-PCR amplicon profiles were the highest in organic and lowest in the perennial pasture grass rotation. Based on multivariate analysis of LH-PCR amplicon profiles using hierarchical cluster analysis and non-metric MultiDimensional Scaling (MDS), soil bacterial communities subjected to continuous tomato production or continuous disk-fallow cultivation were closely related after three years of the different land management practices. Communities in soil left undisturbed under a weed fallow were similar to communities in the perennial pasture grass. Communities in the organically managed system were unique. Following the initiation of tomato production, the similarity decreased between continuous tomato production and continuous disk-fallow cultivation, as well as between the weed fallow and perennial pasture grass rotation. However, communities from weed fallow and disk fallow became more similar. By the end of the tomato production season, communities in the organic system remained unique; whereas communities in the weed fallow and perennial pasture grass rotation became more similar again and closely related to communities under continuous tomato production and continuous disk-fallow cultivation.