Soil plays a crucial role as a significant reservoir for antibiotic resistance genes (ARGs). Despite the extensive research conducted in this area, there remains a need for further investigation, particularly concerning diverse types of agricultural soil. This comprehensive study examined Fusarium wilt diseased and healthy soil samples to investigate the spectrum of ARGs and identify bacteria potentially harboring these genes. The level of antibiotic resistance (AR) in the two soil types was detected by using culture plate counts (PC). We quantified and identified antibiotic resistant bacteria (ARB) against nine antibiotics. From the PC results, the relative number of ARB (number of ARB/total number culturable bacteria) resistant to erythromycin, lincomycin, sulfonamides, streptomycin sulfate, kanamycin, and enrofloxacin in the diseased soil was significantly higher than that in the healthy soil (One-way ANOVA, p < 0.01). The GeoChip (version 5.0) was employed to identify ARGs and antibiotic biosynthetic genes (ABGs). Interestingly, despite the presence of similar ARGs in both soil types, the Fusarium wilt diseased soil demonstrated a significantly elevated abundance of the tetracycline (tetX) resistance gene compared to the healthy soil. A robust correlation (r ≥ 0.8) between multidrug efflux pumps and ARGs indicates that natural antibiotics as selective pressures for transportation mechanisms. Our analysis identified diverse ARB phylotypes and multiple ARGs in both soil types. Incorporating these soil types into ARGs risk assessments and relevant monitoring is essential for a comprehensive understanding of AR dynamics in various environments.