Florida's strawberry production provides significant economic benefit for the State; however, plant-parasitic nematodes (PPNs) pose a significant barrier to production. A better understanding of the distribution of nematode diversity in these fields could help to evaluate the potential risk to crops in agricultural fields and support more sustainable PPN management, but accurate analysis of constituent nematode species is key. The use of targeted mitometagenomics (mtMG) to identify nematode species has shown promise with nematode mock communities, but it remains unclear how it compares in natural agricultural settings and to the more traditional morphology-based approach. In this study, we performed a diversity survey of nematode communities across four different strawberry fields at four depths in the State of Florida using both mtMG and morphological methods. We observed significant differences in nematode community richness and composition between the two methods. Both methods failed to detect taxa recovered by the other method, due to method-specific biases resulting from differential detection of trophic groups. Importantly, both methods did agree on the detection and distribution of Meloidogyne, the most abundant PPNs with the added benefit of the mtMG precisely describing specific species. Despite significant community differences, both methods pointed to the important role of both field and depth in shaping these communities and provided evidence of PPN migration across the soil profile. In conclusion, our findings support the complementary use of multiple detection/identification methods when evaluating nematode diversity, particularly for PPNs.