Cryoconite is a microbe–mineral aggregate which darkens the ice surface of glaciers. Microbial process and marker gene PCR-dependent measurements reveal active and diverse cryoconite microbial communities on polar glaciers. Here, we provide the first report of a cryoconite metagenome and culture-independent study of alpine cryoconite microbial diversity. We assembled 1.2 Gbp of metagenomic DNA sequenced using an Illumina HiScanSQ from cryoconite holes across the ablation zone of Rotmoosferner in the Austrian Alps. The metagenome revealed a bacterially-dominated community, with Proteobacteria (62% of bacterial-assigned contigs) and Bacteroidetes (14%) considerably more abundant than Cyanobacteria (2.5%). Streptophyte DNA dominated the eukaryotic metagenome. Functional genes linked to N, Fe, S and P cycling illustrated an acquisitive trend and a nitrogen cycle based upon efficient ammonia recycling. A comparison of 32 metagenome datasets revealed a similarity in functional profiles between the cryoconite and metagenomes characterized from other cold microbe–mineral aggregates. Overall, the metagenomic snapshot reveals the cryoconite ecosystem of this alpine glacier as dependent on scavenging carbon and nutrients from allochthonous sources, in particular mosses transported by wind from ice-marginal habitats, consistent with net heterotrophy indicated by productivity measurements. A transition from singular snapshots of cryoconite metagenomes to comparative analyses is advocated.