Phylogenetically salient stimuli such as spiders are commonly reported threats in the general population and the most common object of specific phobias in clinical populations. Several theories have hypothesized that our perceptual systems prioritize such stimuli in an “automatic” or “bottom-up” manner due to their evolutionary salience. However, empirical research on the perceptual processing of these stimuli as well as the influence of “top-down” goal-driven and bottom-up stimulus-driven factors is lacking. Here, we used perceptual psychophysics to determine absolute perceptual thresholds for the detection of spider and crab images. Subsequently, participants used spider and crab cues (that imposed a top-down perceptual set) to detect spiders and crab images presented at their predetermined perceptual threshold in a two-alternative forced-choice perceptual decision-making task. While spiders were detected at lower perceptual thresholds than crabs, they were not immune to top-down influence. Indeed, compared to top-down crab cues, spider cues improved the speed and accuracy of detection of spiders vs crabs. Using a hierarchical drift diffusion model, we found that spider cues biased decision-making not only by shifting the starting point of evidence accumulation towards the spider decision, but also by increasing the efficiency with which sensory evidence accumulated, more so for spider than crab perceptual decisions. Overall, these findings provide evidence for the perceptual prioritization of phylogenetically salient stimuli and highlight the computational mechanisms by which this prioritization is facilitated by bottom-up and top-down factors.