Survival of marble goby larvae fed either Rhodovulum sulfidophilum, a phototrophic bacterium cultured from palm oil mill effluent (pPB), or microalgae ( Nannochloropsis sp.) was evaluated at two salinities. Larvae directly fed pPB had survival of 0–29% at 5 g L−1 salinity and 0–19% at 10 g L−1 salinity, whereas larvae directly fed microalgae suffered complete mortality after 20 days of culture at both salinities. However, larvae indirectly fed pPB or microalgae, i.e. via rotifers (Days 1–30) and Artemia nauplii (Days 21–30) cultured solely from pPB or microalgae, showed improved survival of 35–55% or 44–49% at 5 g L−1 salinity respectively. In all experiments, fish larvae reared at 5 g L−1 salinity showed significantly higher (P < 0.01) mean survival than those reared at 10 g L−1 salinity. The survival of larvae fed the bacterial-based diet was higher compared with microalgal diet used in previous studies. The pPB had higher total polyunsaturated fatty acids and docosahexaenoic acid (DHA) than the microalgae, which had very high eicosapentaenoic acid (EPA). Larvae with very high ratios of DHA/EPA (>11) or/and ARA (arachidonic acid)/EPA (>5), attributable to their given diet, however suffered the highest mortality.