Plant parasitic nematodes (PPNs) are widely distributed in all agroecological zones (AEZs) within Kenya. Plant parasitic nematodes are important pests of many cultivated crops and they exert a detrimental influence on a wide range of vascular plants, leading to significant crop losses by reducing both quantity and quality of the yield. However, due to inadequate taxonomic descriptions and a low number of diagnostic features, the morphological diagnosis of many species remains a challenge. The objective of this study was to characterize PPNs associated with sweet potatoes in different agroecological zones of Kirinyaga County, Kenya, using 18S rRNA gene sequencing. Seventy-seven soil samples from sweet potato tubers rhizosphere were collected from different agroecological zones and nematodes were extracted using Baermann’s technique. Thirteen nematode isolates were obtained and only seven could be identified morphologically to their genus level based on their distinct phenotypes. Seven isolates that could not be identified through the microscope were advanced to molecular sequencing. The nematode DNA were extracted and the PCR amplification and sequencing of 18S rRNA gene carried out. The study identified six PPN species, including Mylonchulus hawaiiensis, Aporcelaimellus nigeriensis, Rotylenchulus reniformis, Rotylenchulus borealis, Aporcella femina, Heterodera dunensis, and a predatory nematode (Dorylaimus aff. stagnalis) as part of the soil biota. This study showed significant distribution of plant parasitic nematodes across the agroecological zones. Thus, the occurrence of a nematode species complex in sweet potato farms requires the development of specific and appropriate sustainable control strategies.