This study aims to quantify the utility of allozyme supernatant and formalin-fixed tissue samples for SNP-based analyses using ten specimens of spring salamanders (Gyrinophilus porphyriticus ). We use a target capture approach (RAD-based capture) with replicated sampling (allozyme supernatant, allozyme homogenate pellet, and formalin-fixed tissue) as well as standard RADseq-derived loci from frozen blood of seven of the same ten specimens. In particular we seek to investigate: (1) what factors predict success of allozyme supernatant and formalin-fixed samples to genomic inquiry? (2) How similar are SNP-calls for differently preserved technical replicates? (3) Do replicates for a given specimen yield consistent results across phylogenomic and population genomic analyses? 4) What potential biases are introduced by pooling target-capture and RADseq datasets?