We introduce benchmark signatures to characterize the capacity demands of LLM benchmarks and their overlaps. Signatures are sets of salient tokens from in-the-wild corpora whose model token perplexity, reflecting training exposure, predicts benchmark performance. We extract them via stepwise forward selection with linear regression in a meta-evaluation spanning 32 LLMs and 89 benchmarks across diverse domains. We then analyze how these signatures relate to both the semantic similarity of benchmark questions and the correlation structure of model performance. While performance correlations are uniformly high and semantic overlaps stay in a narrow mid-range, benchmark signatures reveal more nuanced structure. For instance, they uncover substantial overlap between benchmarks in knowledge and reasoning tasks, whereas benchmarks in culture- and humanity-oriented domains show low similarity with each other. Unlike raw performance correlations, which are influenced by benchmark-orthogonal factors such as question formats, signatures are robust to such confounds. We further identify cross-functional overlaps between logic, math, language, instruction following, and cultural/world modeling, with coding emerging as the most isolated function, interacting only moderately with the ability of detecting missing information. Qualitative analysis shows that only the knowledge signature aligns with actual knowledge, suggesting that LLM semantic organization may differ from human conceptual structure. Together, these findings offer insights into benchmark validity, LLM sensitivities, and the landscape of interconnected LLM capacities. We have open-sourced the code and data in this https://github.com/siyangwu1/Benchmark-Signature-Repository.