Genomic imprinting is an epigenetically-regulated process of central importance in mammalian development and evolution. It involves multiple levels of regulation, with spatio-temporal heterogeneity, leading to the context-dependent and parent-of-origin specific expression of a small fraction of the genome. Genomic imprinting studies have therefore been essential to increase basic knowledge in functional genomics, evolution biology and developmental biology, as well as with regard to potential clinical and agrigenomic perspectives. However, suitable molecular and computational tools might be challenging especially in livestock species in which knowledge on genomic imprinting is still sparse. Here, we propose an insight of two technologies (targeting sequencing through short reads vs. genome-wide sequencing through long reads) to detect parent-of-origin methylation with a focus on germline specific differentially methylated regions (DMR). Both studies led in pigs using reciprocal crosses showed a higher rate of genotyping errors and a higher variability of CpG methylation rate with the long read sequencing technology than the capture methyl-seq technology developed by our group. However, when both technologies are concordant, information is more exhaustive using the long read technology thanks to the unambiguous haplotype identification of the two parental origins. Although, analyses need to be deepened, we identified orthologous paternal and maternal DMR as well as pig specific parental DMR. Our results highlight the necessity of complementary sequencing technologies to bring new insights for a better understanding of genomic imprinting mechanisms in livestock species. Moreover, the validation of a dedicated molecular tool in pigs focused on imprinted regions paves the way to novel studies to evaluate the contribution of genomic imprinting mechanisms in the genetic architecture of major agronomic traits.