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Duckweeds (Lemnaceae) are tiny plants that float on aquatic surfaces and are typically isolated from temperate and equatorial regions. Yet, duckweed diversity in Mediterranean and arid regions has been seldom explored. To address this gap in knowledge, we surveyed duckweed diversity in Israel, an ecological junction between Mediterranean and arid climates. We searched for duckweeds in the north and center of Israel on the surface of streams, ponds and waterholes. We collected and isolated 27 duckweeds and characterized their morphology, molecular barcodes (<i>atpF</i>-<i>atpH</i> and <i>psbK</i>-<i>psbI</i>) and biochemical features (protein content and fatty acids composition). Six species were identified—<i>Lemna minor</i>, <i>L. gibba</i> and <i>Wolffia arrhiza</i> dominated the duckweed populations, and together with past sightings, are suggested to be native to Israel. The fatty acid profiles and protein content further suggest that diverged functions have attributed to different haplotypes among the identified species. <i>Spirodela polyrhiza</i>, <i>W. globosa</i> and <i>L. minuta</i> were also identified but were rarer. <i>S. polyrhiza</i> was previously reported in our region, thus, its current low abundance should be revisited. However, <i>L. minuta</i> and <i>W. globosa</i> are native to America and Far East Asia, respectively, and are invasive in Europe. We hypothesize that they may be invasive species to our region as well, carried by migratory birds that disperse them through their migration routes. This study indicates that the duckweed population in Israel’s aquatic environments consists of both native and transient species.