Porcine epidemic diarrhea virus (PEDV) is a fatal epizootic swine coronavirus that presents a financial threat to the global swine industry. Since the discovery of the low-pathogenic genotype 1b (G1b) in 2014, it has been responsible for sporadic outbreaks in South Korea. In this study, we identified novel G1b variants arising from the natural recombination of a major pandemic-like G2b virus and a minor G1b virus currently circulating in the domestic field. The whole-genome sequences of two 2018–19 G1b recombinants, KNU-1808 and KNU-1909, were determined. A genomic comparison showed that these two viruses share the highest nucleotide sequence similarity with the 2017 G1b strain but share less similarity with the 2014 G1b emergent strain KNU-1406. However, the putative recombination breakpoints spanning the first 1,170 nucleotides of the spike (S) gene were almost identical among the emergent and contemporary G1b strains. Recombination detection indicated that the inter-subgroup G1b recombinant first emerged in 2017 by introducing the N-terminal domain of S from KNU-1406 into the backbone of KNU-1703, possibly leading to antigenic shift. It then evolved into KNU-1808 and KNU-1909 through genetic drift, moving toward a more G2b-like genotype. Phylogenetic analysis revealed that the 2018–2019 G1b recombinants belong to a cluster containing other G1b strains but form a new branch. This study provides an important advance warning in regard to the emergence and prevalence of new genotypes or variants that can result from genetic recombination between two different PEDV genotypes circulating in endemic areas and continuous non-lethal mutations essential for viral fitness in the host environment. Electronic supplementary material The online version of this article (10.1007/s00705-020-04767-4) contains supplementary material, which is available to authorized users.