This paper is the first of its kind in Indonesia where effects of artisanal fishing pressure from particular gear types shows an influence on the biomass of reef fish families measured by visual census. Surveys of reef fish communities and benthic variables at 36 fishing grounds, of varying fishing pressure, showed that Scaridae abundance was the factor most influencing fish community structure. The positive relationships between algal turf and reef fish variables and the negative relationships between hard coral cover and three reef fish variables (Scaridae biomass, herbivore biomass and fish species richness) suggests that substrate variables may be used to predict reef fish community variables and that herbivorous fish promote algal turfs at the expense of other benthos. Relationships between reef fish guilds and fishing pressure showed a strong negative impact of muro-ami and gill netting on seven families of reef fish. The strong influence of netting on Caesonidae and Lethrinidae biomass was consistent with the targeting of these families by these fishing methods in Karimunjawa. Both gillnets and muro-ami netting were also negatively correlated with invertivores, a trophic group consisting of a range of reef fish families in Karimunjawa. Although the low biomass of fish populations is likely associated with past and existing fishing practices, negative relationships between fishing pressure indices and reef fish biomass were consistent with the selectivity of families by different fishing gears in Karimunjawa. The implication for management is that both non-selective gears (netting) and selective fishing practices (e.g., handspear and speargun) are capable of modifying the structure of reef fish populations and require active management controls.