Stock assessment of goatfish belonging to two Parupeneus species (P. indicus =882), (P. multifasciatus = 659) from the waters of Iligan Bay, Mindanao Sea, Southern Philippines were collected and investigated. Length-weight relationships and relative condition factors of the species were examined. Population parameters were assessed using FiSAT II software. Growth parameters were estimated by applying the von Bertalanffy growth function. The results showed positive correlations between length and weight. The values of b significantly (P<.000) rose from 2.871 in P. indicus to 3.293 in P. multifasciatus. The condition factors for the species ranged between 1.02 ± 0.21 in P. multifasciatus to 1.028 ± 0.32 in P. indicus. The growth and mortality parameters asymptotic length (L∞), annual growth rate (K), annual total mortality (Z), natural mortality (M), fishing mortality (F) and exploitation rate (E) were 27.30 cm, 1.500, 4.14, 2.40, 1.74 and 0.42 for P. indicus; and 22.05 cm, 1.500, 5.47, 2.55, 2.93 and 0.53 for P. multifasciatus respectively. The exploitation rate (E) of P. indicus species was within the optimal exploitation level, however for the P. multifasciatus exceeded the optimal exploitation level (0.53). A bimodal recruitment pattern of unequal strength was observed for P. multifasciatus while P. indicus displayed a unimodal pattern. The result of the virtual population analysis (VPA) routine showed that most of the small and young fish were prone to natural losses while bigger fish were mostly caught by the fisherman. Finally, the maximum sustainable yield (Emax) for the two species was higher than the exploitation level, indicating that these two goatfish species were in good condition in Iligan Bay.