Restriction site-associated DNA sequencing (RADseq) provides researchers with the ability to record genetic polymorphism across thousands of loci for non-model organisms, potentially revolutionising the field of molecular ecology. However, as with other genotyping methods, RADseq is prone to a number of sources of error that may have consequential effects for population genetic inferences, and these have received only limited attention in terms of the estimation and reporting of genotyping error rates. Here we use individual sample replicates, under the expectation of identical genotypes, to quantify genotyping error in the absence of a reference genome. We then use sample replicates to (1) optimize de novo assembly parameters within the program Stacks, by minimizing error and maximizing the retrieval of informative loci, and; (2) quantify error rates for loci, alleles and SNPs. As an empirical example we use a double digest RAD dataset of a non-model plant species, Berberis alpina, collected from high altitude mountains in Mexico.