The brown sea cucumber fishery is active in the Galapagos Islands since the year 1991 after its collapse in mainland Ecuador. This paper analyzes the Galapagos Sea cucumber fishery over the past decade and the reasons for its management pitfalls and chronic over fishing, and proposes an improved strategy for estimating stock size and harvest potential. Based on the historical distribution of the fishing fleet and past fishery surveys, 15 macrozones were defined; their areas were estimated from the coastline to the 30m isobaths and the numbers of sample replicates per macrozone were calculated for a density estimate precision of ±25%. Overall stock size was calculated by summing over all macrozones and was multiplied by 0.122 to obtain the annual quota. This multiplier was derived by inserting an exploitation rate of E=0.3 and a published natural mortality value of M=0.17 into Cadimas formula, thereby obtaining a more conservative precautionary quota estimate. Pre-fishery stock densities in 2009 were below the legal threshold value and the fishery remained closed. Mean densities were significantly lower in the deeper (&gt;15m) than in the shallower (<15m) stratum, contrary to fishermen expectations. Through an empirical regression of (log) pre-fishery density versus subsequent annual catch for the period 1998-2008 we found that catches of most years greatly exceeded the here proposed quota explaining the collapsed nature of the stock. Rev. Biol. Trop. 60 (2): 539-551. Epub 2012 June 01.