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Abstract Single‐nucleotide polymorphisms (SNPs) are preferred over microsatellite markers in many evolutionary studies, but have only recently been applied to studies of parentage. Evaluations ofSNPs and microsatellites for assigning parentage have mostly focused on special cases that require a relatively large number of heterozygous loci, such as species with low genetic diversity or with complex social structures. We developed 120SNPmarkers from a transcriptome assembled usingRNA‐sequencing of a songbird with the most common avian mating system—social monogamy. We compared the effectiveness of 97 novelSNPs and six previously described microsatellites for assigning paternity in the black‐throated blue warbler,Setophaga caerulescens. We show that the full panel of 97SNPs (meanH_o = 0.19) was as powerful for assigning paternity as the panel of multiallelic microsatellites (meanH_o = 0.86). Paternity assignments using the two marker types were in agreement for 92% of the offspring. Filtering individual samples by a 50% call rate andSNPs by a 75% call rate maximized the number of offspring assigned with 95% confidence usingSNPs. We also found that the 40 most heterozygousSNPs (meanH_o = 0.37) had similar power to assign paternity as the full panel of 97SNPs. These findings demonstrate that a relatively small number of variableSNPs can be effective for parentage analyses in a socially monogamous species. We suggest that the development ofSNPmarkers is advantageous for studies that require high‐throughput genotyping or that plan to address a range of ecological and evolutionary questions.