Peste des petits ruminants (PPR), also known as sheep and goat plague, is the deadliest disease affecting the small ruminant industry and a threat to biodiversity conservation caused by peste des petits ruminants virus (PPRV). Effective elimination of the virus will be mainly supported by the availability of effective vaccines and a wide spectrum of accurate and rapid diagnostic tools. In the light of Global PPR Control and Eradication Programme of 2030, rapid and functional molecular diagnostic tools were actively developed between 1989 and 2019, to allow detailed monitoring of any ongoing PPRV epidemics. The development and use of ultra-rapid reverse transcription polymerase chain reaction (RT-PCR) and its variants and nucleotide sequencing methods is further improving the arsenal of molecular genomic diagnosis of PPR. For instance, in-depth genomic data were mainly generated using Sanger dideoxynucleotide cycle sequencing method and now are being produced using Illumina and recently Oxford nanopore next-generation sequencing technologies due to their higher throughput capabilities, fast turnaround time and lower sequencing costs per sample. This has increased sequence dataset to over 1,800 PPRV nucleotide sequences in the public databases, permitting for more robust and more complex phylogenetic analyses although sequences from non-domestic animals and atypical hosts remain rare. This chapter is elucidating new trends in the field of molecular diagnosis of PPR, with special regard to modern trends in molecular detection and next-generation sequencing.