Cattleya is a genus of Orchidaceae with species distributed throughout the neotropics, especially in Brazil; so far, more than 130 species and 89 nothospecies have been recorded. The overlapping distribution of Cattleya species and the natural crosses dependent on local pollinators allow emerging natural hybrids as a likely mechanism of evolution. Both Cattleya amethystoglossa and C. warneri were previously reported as parentals of independent natural hybrids, however, a natural hybrid involving both species has not been recorded. Here, Cattleya × jequieensis is reported as a natural hybrid between C. amethystoglossa and C. warneri from Bahia (Brazil). Morphological characters reveal a reasonably intermediate phenotype compared to its parental species, including number of internodes, number of flowers per inflorescence, width and length of petals. Sanger sequencing from both psbA-trnH plastid spacer and the nuclear ribosomal DNA Internal Transcribed Spacer (ITS) provide evidence supporting the origin of parentals. This study constitutes a new record of natural hybrids among Cattleya species from Brazil.