From June to December 2003, six monthly samples were performed in Boca Grande estuary and San Juan River estuary in Coiba National Park, Province of Veraguas in order to compare diverstity and abundance of fish species in these estuaries. Physical and chemical parameters were measured. This data indicated that these insular estuaries are use as commercial fishes breeding areas. Five hundred and eighty two (582) fishes were captured, two hundred ninety (290) in Boca Grande estuary and two hundred and ninety two (292) in San Juan River estuary. Six (6) orders were reported, corresponding to twenty (20) families, including thirty (30) genera and fourty four (44) species, distributed as follows: 18 families, 24 genera and 30 species in the Boca Grande estuary and 15 families, 21 general and 29 species in San Juan River estuary. Fifteen species were common to both estuaries. Fifty nine percent (59%) of the species were considered of commercial interest and ninety percent (90%) were juveniles. Atherinella srgentea was the most abundant in Boca Grande estuary and Lile stolifera was the most abundant in San Juan River estuary.