Natural mortality (M) is a key parameter for understanding population dynamics, especially in relation to harvested populations. Direct observations of M in crustaceans are scarce, due to the moulting process. Indirect methods to estimate M with easier-to-obtain life history attributes are therefore used routinely. Given their theoretical background, we reviewed the applicability of these methods for crustaceans. We applied the selected methods to two crustacean species harvested in Chilean waters: the yellow squat lobster (Cervimunida johni) and red squat lobster (Pleuroncodes monodon). Uncertainty of each M estimate was incorporated in the life history parameters that input into the indirect method (trait-error) and parameters defining the indirect method (coefficient-trait-error). Methods based on the relationship between total mortality and maximum age, or with different ages and based on life history theory were the most appropriate for crustaceans since they apply across taxa. M estimates showed high variability between species, sexes and areas. Estimations of M for C. johni varied from 0.13 to 0.28 (year−1) for males and 0.17 to 0.51 (year−1) for females. For P. monodon values for the north varied from 0.26 to 0.37 (year−1) for males and 0.24 to 0.45 (year−1) for females. In the south, values of M were higher for both males (0.43–0.68 year−1) and females (0.41–1.06 year−1). High variability in the M estimates was associated with the method and number of parameters, their uncertainty, theoretical background and probability distribution. M estimates are not comparable, raising the need to propagate the uncertainty of M into the stock assessment of Chilean squat lobsters.