Understanding the impact of collection and storage preservatives is important for all specimen-based research, ranging from morphological studies to genetic- and genomic-based research. We evaluated the effectiveness of four commonly used preservatives for their ability to preserve insect DNA for several ant species as well as the DNA from host-associated microbes of one ant species. We made replicated collections of ant specimens of different sizes and from three different environmental climates into four different preservatives (95% ethanol, dimethyl sulfoxide (DMSO), propylene glycol and RNAlater), isolated DNA across two different time periods and performed PCR on all DNA extracts (n = 180 samples   10 controls). Although ethanol returned the best overall results for DNA yield and PCR success, our analyses did not show a significant difference between specimens preserved in ethanol or propylene glycol on the timescales we investigated. We found that average DNA yield was significantly higher when specimens were originally collected in ethanol instead of DMSO, propylene glycol, or RNAlater™ (Applied Biosystems/Ambion). PCR results for both the insect and endosymbiotic bacteria showed a significant advantage for preserving ants in ethanol or propylene glycol over DMSO or RNAlater for room temperature storage. Our findings suggest that collection of insect specimens into ethanol is the preferred method for preserving host and host-associated bacterial DNA, but that propylene glycol is a suitable alternative when ethanol is not available or permitted.