Gastrointestinal zoonotic helminths of dogs and cats have a public health concern worldwide. We investigated the prevalence of gastrointestinal helminths of zoonotic significance in dogs and cats in lower Northern Thailand and utilized molecular tools for species identification of hookworms and Opisthorchis viverrini. Fecal samples of 197 dogs and 180 cats were collected. Overall prevalence of infection using microscopy was 40.1% in dogs and 33.9% in cats. Helminth infection found in both dogs and cats included hookworms, Spirometra spp., Taenia spp., Toxocara spp., O. viverrini, Strongyloides spp. and Trichuris spp. Hookworms were the most common helminth in dogs, while Spirometra spp. were the most prevalent in cats. Among hookworm infection in dogs and cats, Ancylostoma ceylanicum was the most prevalent hookworm, being 82.1% in hookworm infected dogs and 95.8% in hookworm infected cats. Mixed-infection due to hookworms and Spirometra spp. was the most dominant in both dogs and cats. Our finding showed that zoonotic helminth infection is highly prevalent in dogs and cats in the lower Northern area of Thailand.