Knowledge about the underlying genetic architecture of phenotypic traits is needed to understand and predict their evolutionary dynamics. The number of causal loci, magnitude of their effects and location in the genome is however still largely unknown. Here we use genome-wide SNP data from two large-scale datasets on house sparrows and collared flycatchers to examine the genetic architecture of different morphological traits (tarsus length, wing length, body mass, bill depth, bill length, total and visible badge size and white wing patches). Genomic heritabilities were estimated using relatedness calculated from SNPs. The proportion of variance captured by the SNPs (SNP-based heritability) was lower in house sparrows compared to collared flycatchers, as expected given marker density (6,348 SNPs in house sparrows versus 38,689 SNPs in collared flycatchers). Indeed, after down-sampling to similar SNP density and sample size this estimate was no longer markedly different between species. Chromosome partitioning analyses demonstrated that the proportion of variance explained by each chromosome was significantly positively related to the chromosome size for some traits, and, generally, that larger chromosomes tended to explain proportionally more variation than smaller chromosomes. Finally, we found two genome-wide significant associations with very small effect sizes. One SNP on chromosome 20 was associated with bill length in house sparrows and explained 1.2% of phenotypic variation (VP) and one SNP on chromosome 4 was associated with tarsus length in collared flycatchers (3% of VP). Although we cannot exclude the possibility of undetected large-effect QTL, our results indicate a polygenic basis for morphological traits.