Morels are edible fungi collected for food and medicines worldwide. In the present study, samples of Morchella were collected during consecutive fungal surveys in 2017-2021 from Neelum Valley, Azad Jammu, and Kashmir. The specimens were identified as Morchella costata Pers., Morchella conica Krombh., Naturgetr. Abbild. Beschr., Morchella deliciosa Fr., Morchella elata Fr., and Morchella tridentina Bres., after phylogenetic sequencing using the nuclear ribosomal DNA (nrDNA) barcoding technique along with morpho-anatomical analyses. The highest stipe length was found in Morchella elata (6-8.8 cm), and the lowest was noted in Morchella deliciosa (2-3.5 cm). The highest pileus length was found in Morchella costata (6.9-12 cm), and the lowest was noted in Morchella conica (2.5-4 cm). The highest spore size was observed in Morchella costata (26.5-33 × 12-16 μm), and the lowest was observed in Morchella conica (7.2-7.5 × 12.5-14.6 μm). This is the first detailed study on morels, based on molecular phylogeny from the State of Azad Jammu and Kashmir (AJK), Pakistan. Variations have been observed in both qualitative and quantitative characters. The results reinforced the significance of the morpho-anatomical features of the genus Morchella and will be used as an aid for valuable taxonomic tools in the systematics of morels. The accurate identification of morels species is very crucial for the isolation of bioactive compounds, and these compounds play a vital role in the drug discovery. So, we recommend a comprehensive exploration of Morels in the Western Himalayan Forests by using advanced molecular approaches and the isolation of bioactive compounds because this genus is still unexplored in the context of pharmaceutics.