Citrus fruits are attacked by several fungal pathogens during post-harvest storage in Pakistan. The survey of fruit markets of Faisalabad, Multan, and Sargodha, Pakistan indicated that several fungal pathogens from different Genera including Fusarium, Geotrichum, Penicillium, Alternaria, Lasiodiplodia, Aspergillus and Rhizopus are infecting citrus fruits. The incidence of Penicillium rot was highest at all locations during 2016-17. All pathogens were identified based on the internal transcribed spacer (ITS) region. Alternaria and Fusarium species were also amplified and sequenced based on endopolygalacturonase EndoPG and translation elongation factor gene. The most predominantly occurring Genera were Penicillium, Fusarium and Geotrichum with the overall prevalence of 42.6, 14.2 and 12.2%. Phylogenetic relationships of these genera based on the ITS region with species from other geographical regions of the world showed diverse ancestral relationships. Most predominantly occurring species of Penicillium viz., P. italicum and P. digitatum were selected to conduct management studies. The effect of resistance inducers salicylic acid SA and jasmonic acid JA at different concentrations revealed that SA and JA inhibited the disease development on citrus fruits ‘Kinnow’, ‘Meyer lemon’ and ‘Mosambi’ in a concentration-dependent manner. The activity of peroxidase (POD) and polyphenol oxidase (PPO) also showed an upsurge in the activity of both enzymes compared to untreated and healthy fruits. The effect of plant extracts S. aromaticum, C. citratus, C. longa, C. verum and E. cardamomum was tested in vitro on colony growth inhibition of P. digitatum and P. italicum. S. aromaticum and C. verum produced the highest inhibition of colony growth of both pathogens at 15g/L. Total phenolic contents (TPC) and total flavonoid contents (TFC) were found to be highest in S. aromaticum. RP-HPLC analysis for the presence of antifungal phenols and flavonoids (quercetin, gallic acid, benzoic acid, chlorogenic acid, gallic acid, ferulic acid, vanillic acid, syringic acid, cinnamic acid, kaempferol, sinapinic acid) indicated that quercetin, kaempferol, and gallic acid were present in all plant extracts. S. aromaticum and C. verum showed the highest concentration of detected phenols and flavonoids. The combined effect of S. aromaticum, C. verum and SA and JA on ‘Kinnow’, ‘Meyer lemon’ and ‘Mosambi’ fruits revealed that the activity of these treatments was significantly enhanced when applied together. The combination of S. aromaticum with SA and JA produced the lowest disease incidence and severity (%) of green and blue mold on all types of fruits compared to infected control and other treatments. The activity of PPO and POD was significantly enhanced in fruits treated with combined application of plant extracts and resistance inducers than infected control. The effect of treatments on quality parameters such as total soluble solids, weight loss, ascorbic acid content, juice content loss, and titratable acidity showed significant variation in all treatments. It was concluded that resistance inducers and plant extracts as a stand-alone and combined treatments can suppress green and blue mold and cause an upsurge in the activity of PPO and POD. The increase in activity of PPO and POD enzymes might have a role in the suppression of green and blue mold of citrus fruits.