The diatoms of Lekki lagoon for the first time were studied at monthly intervals for two years (June 2003-May 2005). Two hundred and thirty seven (203 pennate and 34 centric forms) diatom species belonging to 50 genera were recorded. Among the pennate diatoms, the most frequent species were Achnanthes conspicua, Bachysira follis, Bacillaria paradoxa, Craticula cuspidata, Cymbella ventricosa, Decussata placentula, Eunotia incisa, Frustulia rhomboides, Gyrosigma balticum, Luticola mutica, Nitzschia radiosa, Pinnularia biceps, P. gibba, Placoneis exigua, Plagiotropis sp., Sellophora pupila and Synedra ulna var. longissima. The holoplanktonic forms included Synedra ulna (Nitz.) Ehr., Synedra acus Kutzing and Tabellaria fenestrata (Lyng.) Kutzing. The centrals were ably represented by Aulacoseira and its varieties, Cyclotella and Terpsinoe musica. In this study, fifty new diatoms species were recorded for Lagos lagoon complex while Aulacoseira herzogii is new record for Nigeria. Community structure analysis shows a highly diverse environment.