The citrus leafminer (CLM), Phyllocnistis citrella Stainton causes injury to citrus and related species in the Rutaceae family. The damage that the CLM larvae can cause is significant in citrus plantations. We tested two citrus cultivars — ‘Kinnow’ (Citrus reticulata Blanco) and ‘Fairchild’ (a hybrid of Citrus reticulata Clementine x Orlando Tangelo) — to quantify CLM larvae infestation and effect on the physiology of the citrus cultivars. We then compared the CLM larval weight with its associated damage. To calculate infestation level, mine area and total leaf area, we used the image analysis technique. The infestation level of CLM was higher in ‘Fairchild’ than in ‘Kinnow’ cultivar of citrus. For both cultivars, larval weight of CLM was directly proportional to the amount of mines generated. Taken together, the results of this study suggest that the mines that CLM larvae generate pose significant effect on the net photosynthetic rates and water use efficiency of citrus nursery plants. These results will help improve our understanding of the interaction between CLM and citrus nursery plants and effect of the pest on the yield potential of the crop.