Circular RNAs (circRNAs) serve as covalently closed single-stranded RNAs and have been proposed to influence plant development and stress resistance. Grapevine is one of the most economically valuable fruit crops cultivated worldwide and is threatened by various abiotic stresses. Herein, we reported that a circRNA (Vv-circPTCD1) processed from the second exon of the pentatricopeptide repeat family genePTCD1was preferentially expressed in leaves and responded to salt and drought but not heat stress in grapevine. Additionally, the second exon sequence ofPTCD1was highly conserved, but the biogenesis ofVv-circPTCD1is species-dependent in plants. It was further found that the overexpressedVv-circPTCD1can slightly decrease the abundance of the cognate host gene, and the neighboring genes are barely affected in the grapevine callus. Furthermore, we also successfully overexpressed theVv-circPTCD1and found that theVv-circPTCD1deteriorated the growth during heat, salt, and drought stresses inArabidopsis. However, the biological effects on grapevine callus were not always consistent with those ofArabidopsis. Interestingly, we found that the transgenic plants of linear counterpart sequence also conferred the same phenotypes as those of circRNA during the three stress conditions, no matter what species it is. Those results imply that although the sequences are conserved, the biogenesis and functions ofVv-circPTCD1are species-dependent. Our results indicate that the plant circRNA function investigation should be conducted in homologous species, which supports a valuable reference for further plant circRNA studies.